Variant report

Variant	rs3000
Chromosome Location	chr4:57777945-57777946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57772971..57776902-chr4:57777481..57784789,10	MCF-7	breast:
2	chr4:57772988..57775343-chr4:57776220..57778579,3	MCF-7	breast:
3	chr4:57774412..57776864-chr4:57776976..57782053,6	K562	blood:
4	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10008356	0.93[ASN][1000 genomes]
rs10030913	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866440	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866441	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1105434	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1107675	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11133472	0.87[GIH][hapmap];0.90[TSI][hapmap]
rs11133474	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11730321	0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11730476	0.90[ASN][1000 genomes]
rs11730525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734953	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736192	0.88[ASN][1000 genomes]
rs11736869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11736965	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737689	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11932673	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11933908	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941568	0.90[EUR][1000 genomes]
rs12500454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501224	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12501990	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502076	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap]
rs13108245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13116564	0.97[ASN][1000 genomes]
rs13119525	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13131605	0.85[ASN][1000 genomes]
rs13136432	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13146960	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149162	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150593	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152476	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13353552	0.96[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap]
rs17081937	1.00[JPT][hapmap]
rs17087317	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1718839	1.00[JPT][hapmap]
rs1877669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963666	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002153	0.94[ASN][1000 genomes]
rs2014870	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2090962	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170073	0.82[CEU][hapmap]
rs2228991	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2412772	0.96[CEU][hapmap];0.92[TSI][hapmap]
rs34124552	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34448457	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35267092	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3733306	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs3796528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3806745	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4276341	0.97[ASN][1000 genomes]
rs4339274	0.82[CEU][hapmap]
rs4864606	1.00[ASN][1000 genomes]
rs4864607	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864608	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865156	0.90[ASN][1000 genomes]
rs4865157	0.93[ASN][1000 genomes]
rs4865158	0.92[ASN][1000 genomes]
rs4865159	0.94[ASN][1000 genomes]
rs4865160	0.94[ASN][1000 genomes]
rs4865172	0.88[CEU][hapmap]
rs55822707	0.98[ASN][1000 genomes]
rs56122758	0.91[ASN][1000 genomes]
rs62308110	0.90[ASN][1000 genomes]
rs62308111	0.90[ASN][1000 genomes]
rs62308135	1.00[ASN][1000 genomes]
rs62308136	1.00[ASN][1000 genomes]
rs62308137	0.99[ASN][1000 genomes]
rs62308155	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554393	0.93[ASN][1000 genomes]
rs6554394	0.93[ASN][1000 genomes]
rs6554397	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554399	0.81[ASN][1000 genomes]
rs6816950	0.90[ASN][1000 genomes]
rs6835102	0.88[ASN][1000 genomes]
rs6835108	0.88[ASN][1000 genomes]
rs6838948	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839845	0.88[ASN][1000 genomes]
rs6840805	0.90[ASN][1000 genomes]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6854420	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855212	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6857005	0.88[ASN][1000 genomes]
rs6857226	0.88[ASN][1000 genomes]
rs6858216	0.90[ASN][1000 genomes]
rs71601656	0.84[ASN][1000 genomes]
rs729844	0.97[ASN][1000 genomes]
rs73242609	1.00[ASN][1000 genomes]
rs7661194	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7666804	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667302	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667744	0.90[EUR][1000 genomes]
rs7680140	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs7680734	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695970	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697176	0.82[CEU][hapmap]
rs781666	1.00[JPT][hapmap]
rs781668	1.00[JPT][hapmap]
rs899630	0.90[EUR][1000 genomes]
rs899631	0.90[EUR][1000 genomes]
rs899632	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9684742	0.97[ASN][1000 genomes]
rs9685436	0.82[CEU][hapmap]
rs9942208	0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3000	IGFBP7	cis	multi-tissue	Pritchard
rs3000	KIAA1211	cis	parietal	SCAN
rs3000	TXNDC9	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57775800-57786200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57776000-57778000	Enhancers	Stomach Mucosa	stomach
3	chr4:57776000-57778200	Enhancers	Small Intestine	intestine
4	chr4:57776200-57778000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr4:57776200-57778200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:57776200-57778200	Enhancers	Brain Hippocampus Middle	brain
7	chr4:57776200-57778200	Enhancers	Brain Substantia Nigra	brain
8	chr4:57776200-57778200	Enhancers	Colon Smooth Muscle	Colon
9	chr4:57776200-57781200	Enhancers	Adipose Nuclei	Adipose
10	chr4:57776400-57778200	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:57776400-57778200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr4:57776400-57780800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:57776400-57784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:57776400-57789400	Weak transcription	Right Ventricle	heart
15	chr4:57776600-57778000	Enhancers	Stomach Smooth Muscle	stomach
16	chr4:57776600-57778800	Genic enhancers	Fetal Muscle Leg	muscle
17	chr4:57776600-57778800	Enhancers	Right Atrium	heart
18	chr4:57776800-57778000	Genic enhancers	Fetal Stomach	stomach
19	chr4:57776800-57778000	Enhancers	Gastric	stomach
20	chr4:57776800-57778200	Enhancers	Esophagus	oesophagus
21	chr4:57776800-57778200	Enhancers	Ovary	ovary
22	chr4:57776800-57778400	Transcr. at gene 5' and 3'	Dnd41	blood
23	chr4:57776800-57778800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:57776800-57779000	Enhancers	Pancreas	Pancrea
25	chr4:57776800-57779400	Enhancers	Lung	lung
26	chr4:57776800-57780400	Genic enhancers	Fetal Thymus	thymus
27	chr4:57777000-57778000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
28	chr4:57777000-57778000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:57777000-57778000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:57777000-57778200	Genic enhancers	Fetal Intestine Small	intestine
31	chr4:57777000-57778200	Genic enhancers	Left Ventricle	heart
32	chr4:57777000-57778200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
33	chr4:57777000-57778400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
34	chr4:57777000-57778400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:57777000-57778800	Enhancers	Primary hematopoietic stem cells	blood
36	chr4:57777000-57779400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:57777000-57779800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:57777000-57784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:57777000-57785400	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr4:57777000-57786400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:57777000-57795800	Weak transcription	A549	lung
42	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
43	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:57777200-57778000	Genic enhancers	H9 Cell Line	embryonic stem cell
45	chr4:57777200-57778000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:57777200-57778000	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:57777200-57778000	Genic enhancers	Fetal Lung	lung
48	chr4:57777200-57778200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:57777200-57778200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr4:57777200-57778200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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