Variant report

Variant	rs9809247
Chromosome Location	chr3:112267523-112267524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112265548..112268745-chr3:112278905..112281998,3	K562	blood:
2	chr3:112259312..112262688-chr3:112264103..112268109,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10755071	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11706550	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1512005	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1512006	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844089	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877363	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994713	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2101632	0.82[EUR][1000 genomes]
rs2131008	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2172196	0.82[EUR][1000 genomes]
rs2279532	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2280066	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2464611	0.84[AMR][1000 genomes]
rs2633555	0.87[EUR][1000 genomes]
rs2633578	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633580	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633582	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633584	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638016	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638017	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638018	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638022	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638031	0.84[AMR][1000 genomes]
rs2638037	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638042	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638045	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668220	0.82[EUR][1000 genomes]
rs2668222	0.82[EUR][1000 genomes]
rs2668223	0.82[EUR][1000 genomes]
rs2705517	0.82[EUR][1000 genomes]
rs2705531	0.93[EUR][1000 genomes]
rs2705532	0.87[EUR][1000 genomes]
rs2705534	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2705566	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28866814	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2933142	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2952323	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2952326	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952327	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34233684	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3732815	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682413	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5000995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772077	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6774355	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792947	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652377	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs766968	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9288954	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9756562	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9848054	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854043	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866734	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869455	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869579	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers 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 target site	39 gene(s)	inside rSNPs	diseases
8	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9809247	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
6	chr3:112244400-112278200	Weak transcription	K562	blood
7	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
8	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:112247000-112267800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:112249200-112269800	Weak transcription	Psoas Muscle	Psoas
14	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
15	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
16	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
18	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
19	chr3:112249200-112279600	Weak transcription	Gastric	stomach
20	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:112249400-112270000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:112249400-112279600	Weak transcription	Lung	lung
24	chr3:112251000-112274200	Weak transcription	Brain Angular Gyrus	brain
25	chr3:112251200-112268200	Strong transcription	Liver	Liver
26	chr3:112252200-112270200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:112252400-112269800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
29	chr3:112253000-112273400	Weak transcription	Brain Substantia Nigra	brain
30	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:112254200-112273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:112257600-112274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:112258800-112268000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:112259200-112270400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:112259600-112268600	Strong transcription	Placenta	Placenta
36	chr3:112259800-112269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:112260000-112271200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:112260000-112278200	Weak transcription	Fetal Brain Male	brain
39	chr3:112260200-112268200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:112260400-112267800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:112260400-112279600	Weak transcription	Pancreas	Pancrea
42	chr3:112261200-112269800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:112261400-112270200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:112261600-112268000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:112262200-112267800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:112262200-112267800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:112262200-112267800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:112262200-112268000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr3:112262200-112268600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:112262200-112270200	Strong transcription	GM12878-XiMat	blood

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