Variant report

Variant	rs7542685
Chromosome Location	chr1:227730453-227730454
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
2	chr1:227728970..227731707-chr1:227751101..227754291,3	MCF-7	breast:
3	chr1:227726703..227728573-chr1:227729012..227731358,2	K562	blood:
4	chr1:227729010..227735281-chr1:227748522..227752811,6	MCF-7	breast:
5	chr1:227725578..227727494-chr1:227729728..227731720,2	MCF-7	breast:
6	chr1:227728577..227730296-chr1:227730401..227732480,2	MCF-7	breast:
7	chr1:227730297..227731134-chr12:34260025..34260625,2	MCF-7	breast:
8	chr1:227729455..227731523-chr1:227733555..227735249,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202264	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1021553	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1021554	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10495276	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799423	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799431	0.82[EUR][1000 genomes]
rs10799432	0.83[EUR][1000 genomes]
rs10799433	0.82[EUR][1000 genomes]
rs10799434	0.82[EUR][1000 genomes]
rs10799435	0.82[EUR][1000 genomes]
rs10916158	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916159	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916165	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916169	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916175	0.82[EUR][1000 genomes]
rs10916176	0.82[EUR][1000 genomes]
rs10916179	0.82[EUR][1000 genomes]
rs10916182	0.81[EUR][1000 genomes]
rs10916183	0.82[EUR][1000 genomes]
rs10916184	0.82[EUR][1000 genomes]
rs10916185	0.81[EUR][1000 genomes]
rs10916187	0.82[EUR][1000 genomes]
rs11484723	0.81[EUR][1000 genomes]
rs11580570	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12023298	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12025815	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12040302	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070002	0.82[EUR][1000 genomes]
rs12070036	0.82[EUR][1000 genomes]
rs12079123	0.82[EUR][1000 genomes]
rs12080321	0.83[EUR][1000 genomes]
rs12132444	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12740317	0.81[AMR][1000 genomes]
rs1495842	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1495845	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1495847	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1845758	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018401	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2088210	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088211	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2088212	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2088214	0.88[AMR][1000 genomes]
rs2093609	0.82[EUR][1000 genomes]
rs2093610	0.82[EUR][1000 genomes]
rs2132367	0.82[EUR][1000 genomes]
rs2201571	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2644140	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28407112	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2935145	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2935146	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2935147	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2935152	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2935155	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2999741	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2999743	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2999744	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2999745	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2999746	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3010183	0.88[AMR][1000 genomes]
rs3010186	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3010190	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3010191	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3010192	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3010193	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3010194	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3010195	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3010196	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4359006	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653512	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653514	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653515	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653848	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653849	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653850	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653853	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6664682	0.82[EUR][1000 genomes]
rs6671825	0.82[EUR][1000 genomes]
rs6697867	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7512348	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7523915	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7528094	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539914	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7551459	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs903683	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs903684	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs903690	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs903697	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs951083	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs976959	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227729200-227730600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:227729200-227731000	Active TSS	Colonic Mucosa	Colon
3	chr1:227729400-227730600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:227729400-227730600	Active TSS	Fetal Intestine Large	intestine
5	chr1:227729400-227730600	Active TSS	Fetal Stomach	stomach
6	chr1:227729400-227730600	Active TSS	Left Ventricle	heart
7	chr1:227729400-227730600	Active TSS	Osteobl	bone
8	chr1:227729400-227730800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:227729400-227730800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:227729400-227730800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr1:227729400-227730800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:227729400-227730800	Active TSS	Psoas Muscle	Psoas
13	chr1:227729400-227730800	Active TSS	Right Atrium	heart
14	chr1:227729400-227730800	Active TSS	HSMM	muscle
15	chr1:227729400-227730800	Active TSS	NHLF	lung
16	chr1:227729400-227731000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:227729400-227731000	Enhancers	Stomach Mucosa	stomach
18	chr1:227729400-227731200	Enhancers	Fetal Brain Male	brain
19	chr1:227729600-227730600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:227729600-227730600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:227729600-227730600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:227729600-227730600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:227729600-227730600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr1:227729600-227730600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:227729600-227730600	Active TSS	Brain Hippocampus Middle	brain
26	chr1:227729600-227730600	Active TSS	Brain Substantia Nigra	brain
27	chr1:227729600-227730600	Weak transcription	Fetal Heart	heart
28	chr1:227729600-227730600	Active TSS	Ovary	ovary
29	chr1:227729600-227730600	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:227729600-227730600	Active TSS	A549	lung
31	chr1:227729600-227730600	Flanking Active TSS	HMEC	breast
32	chr1:227729600-227730600	Active TSS	NHDF-Ad	bronchial
33	chr1:227729600-227730800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:227729600-227730800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:227729600-227730800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr1:227729600-227730800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:227729600-227730800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:227729600-227730800	Active TSS	HSMMtube	muscle
39	chr1:227729600-227731000	Active TSS	Brain Angular Gyrus	brain
40	chr1:227729800-227730600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:227729800-227730600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:227729800-227730600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr1:227729800-227730600	Active TSS	Liver	Liver
44	chr1:227729800-227730600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:227729800-227730600	Active TSS	Esophagus	oesophagus
46	chr1:227729800-227730600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227729800-227730600	Active TSS	Fetal Intestine Small	intestine
48	chr1:227729800-227730600	Active TSS	Fetal Lung	lung
49	chr1:227729800-227730600	Active TSS	Pancreas	Pancrea
50	chr1:227729800-227730600	Active TSS	Skeletal Muscle Male	skeletal muscle

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