Variant report

Variant	rs2501550
Chromosome Location	chr9:140520539-140520540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:140519393..140522407-chr9:140523335..140527001,5	MCF-7	breast:
2	chr9:140513124..140515573-chr9:140519172..140522575,5	K562	blood:
3	chr9:140520368..140523590-chr9:140524404..140528000,5	K562	blood:
4	chr9:140519645..140523590-chr9:140526467..140528234,3	K562	blood:
5	chr9:140512926..140516965-chr9:140518236..140522251,5	MCF-7	breast:
6	chr9:140473487..140475608-chr9:140520167..140523048,2	K562	blood:
7	chr9:140513993..140515601-chr9:140519538..140521041,2	K562	blood:

Variant related genes	Relation type
ENSG00000181090	Chromatin interaction
ENSG00000203993	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116052	0.84[AMR][1000 genomes]
rs10120250	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1045777	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780180	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10867034	0.80[ASN][1000 genomes]
rs11137135	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11137136	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11137155	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11137156	0.98[ASN][1000 genomes]
rs11137157	0.82[ASN][1000 genomes]
rs11137161	0.80[ASN][1000 genomes]
rs11137163	0.80[ASN][1000 genomes]
rs12683290	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13286765	0.82[ASN][1000 genomes]
rs13287726	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1776776	0.81[AMR][1000 genomes]
rs1891628	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2094623	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2257839	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2282020	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2297004	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2297005	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2297006	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2353770	0.80[ASN][1000 genomes]
rs2480116	0.96[ASN][1000 genomes]
rs2488588	0.86[ASN][1000 genomes]
rs2501552	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2501553	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2501554	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2501566	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2501567	0.80[ASN][1000 genomes]
rs2501568	0.80[ASN][1000 genomes]
rs2987618	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34249205	0.90[ASN][1000 genomes]
rs35374891	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3763610	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4246177	0.83[AMR][1000 genomes]
rs4962227	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67089520	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67499662	0.92[ASN][1000 genomes]
rs67789600	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7043932	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71510836	0.92[ASN][1000 genomes]
rs7389975	0.83[AMR][1000 genomes]
rs8181211	0.82[ASN][1000 genomes]
rs821313	0.92[ASN][1000 genomes]
rs821317	0.82[AMR][1000 genomes]
rs863701	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs864747	0.83[AMR][1000 genomes]
rs9410034	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9410111	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9410112	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs950078	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9774907	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
4	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
5	nsv1047563	chr9:140219047-140560852	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv540357	chr9:140219047-140560852	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv531602	chr9:140240417-140535223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	diseases
8	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
10	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
11	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
12	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
13	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
14	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
15	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
16	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
17	nsv616022	chr9:140372570-140523429	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	n/a
18	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
19	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
20	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
21	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
22	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
23	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
24	nsv616024	chr9:140414410-140536098	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
25	nsv831763	chr9:140439831-140614021	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
26	esv3398333	chr9:140451462-140814795	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	n/a
27	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
28	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
29	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	n/a
30	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
31	nsv894665	chr9:140469600-140523429	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	n/a
32	nsv531668	chr9:140492807-140986221	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	n/a
33	nsv894670	chr9:140503095-140526439	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	n/a
34	nsv531669	chr9:140514663-140852911	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2501550	EHMT1	cis	Whole Blood	GTEx
rs2501550	DPH7	cis	Thyroid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140514400-140525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:140515400-140524400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:140515600-140523000	Weak transcription	Psoas Muscle	Psoas
4	chr9:140515600-140523000	Weak transcription	Right Atrium	heart
5	chr9:140515600-140526600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:140515600-140535400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:140515600-140539800	Weak transcription	HMEC	breast
8	chr9:140515800-140522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:140515800-140522400	Weak transcription	Ovary	ovary
10	chr9:140515800-140522600	Weak transcription	Fetal Lung	lung
11	chr9:140515800-140522600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:140515800-140523000	Weak transcription	HUVEC	blood vessel
13	chr9:140515800-140525200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:140515800-140526400	Weak transcription	Fetal Kidney	kidney
15	chr9:140516000-140520800	Weak transcription	Gastric	stomach
16	chr9:140516000-140522400	Weak transcription	Placenta	Placenta
17	chr9:140516000-140522400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:140516000-140522400	Weak transcription	HSMM	muscle
19	chr9:140516000-140522400	Weak transcription	NHLF	lung
20	chr9:140516000-140522600	Weak transcription	Small Intestine	intestine
21	chr9:140516000-140525000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:140516000-140525200	Weak transcription	Pancreas	Pancrea
23	chr9:140516000-140526600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:140516000-140532200	Weak transcription	NHEK	skin
25	chr9:140516000-140533200	Weak transcription	Esophagus	oesophagus
26	chr9:140516200-140521200	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:140516200-140521400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:140516200-140522400	Weak transcription	Stomach Mucosa	stomach
29	chr9:140516200-140522600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:140516200-140522600	Weak transcription	NHDF-Ad	bronchial
31	chr9:140516200-140522800	Weak transcription	Hela-S3	cervix
32	chr9:140516200-140524200	Weak transcription	HepG2	liver
33	chr9:140516200-140524400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:140516200-140525000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:140516200-140526200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:140516200-140527200	Weak transcription	Aorta	Aorta
37	chr9:140516200-140558800	Weak transcription	NH-A	brain
38	chr9:140516400-140520800	Weak transcription	K562	blood
39	chr9:140516400-140522200	Weak transcription	Fetal Thymus	thymus
40	chr9:140516400-140522400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:140516400-140522600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:140516400-140524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:140516400-140524600	Weak transcription	A549	lung
44	chr9:140516400-140526400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:140516400-140526400	Weak transcription	Fetal Brain Female	brain
46	chr9:140516400-140535200	Weak transcription	Fetal Intestine Large	intestine
47	chr9:140517000-140522400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:140517000-140522400	Weak transcription	Colon Smooth Muscle	Colon
49	chr9:140517000-140522600	Weak transcription	Brain Anterior Caudate	brain
50	chr9:140517200-140522400	Weak transcription	Lung	lung

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