Variant report

Variant	rs7651721
Chromosome Location	chr3:101393583-101393584
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
2	chr3:101391957..101394072-chr3:101395408..101397212,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066422	Chromatin interaction
ENSG00000081154	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1031710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs11710533	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.89[ASN][1000 genomes]
rs11714444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11717046	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11718446	0.81[JPT][hapmap]
rs11720745	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923273	0.83[AMR][1000 genomes]
rs11924013	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633089	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs12635128	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs13066768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs13085776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs13094753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1460097	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs17345528	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs17411983	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs2303474	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs34624546	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762729	0.95[JPT][hapmap]
rs3804775	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3804778	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3806653	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342086	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs55654108	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59596156	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62284162	0.82[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997739	0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS 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	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7651721	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs7651721	NXPE3	cis	Esophagus Muscularis	GTEx
rs7651721	ZBTB11	cis	cerebellum	SCAN
rs7651721	NIT2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:101371000-101394800	Weak transcription	Small Intestine	intestine
4	chr3:101373200-101393800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:101373200-101394000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:101374200-101394600	Weak transcription	Esophagus	oesophagus
7	chr3:101382600-101393800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:101383000-101395000	Weak transcription	Spleen	Spleen
9	chr3:101383400-101394000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:101383400-101394200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:101383600-101394800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:101384400-101393800	Weak transcription	Fetal Heart	heart
13	chr3:101384400-101393800	Weak transcription	Right Ventricle	heart
14	chr3:101384400-101394000	Weak transcription	Brain Germinal Matrix	brain
15	chr3:101384600-101394000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:101384600-101394000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:101384600-101394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:101384600-101394400	Weak transcription	HSMMtube	muscle
19	chr3:101384800-101394400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:101385000-101394400	Weak transcription	Lung	lung
21	chr3:101385400-101393800	Weak transcription	NHLF	lung
22	chr3:101386200-101393600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:101386200-101394400	Weak transcription	Ovary	ovary
24	chr3:101386400-101394200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:101386600-101394400	Weak transcription	Psoas Muscle	Psoas
26	chr3:101387400-101393800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:101387400-101394000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:101387600-101393800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:101388200-101394600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:101388600-101394400	Weak transcription	Colonic Mucosa	Colon
31	chr3:101388800-101394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:101389000-101394400	Weak transcription	Fetal Stomach	stomach
33	chr3:101389800-101394400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:101389800-101394400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:101390000-101393800	Weak transcription	HUVEC	blood vessel
36	chr3:101390200-101393600	Weak transcription	Fetal Intestine Large	intestine
37	chr3:101390200-101393800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:101390200-101393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:101390200-101394000	Weak transcription	NH-A	brain
40	chr3:101390200-101394200	Weak transcription	Fetal Kidney	kidney
41	chr3:101390200-101394600	Weak transcription	Aorta	Aorta
42	chr3:101390400-101393800	Weak transcription	Fetal Lung	lung
43	chr3:101390400-101393800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:101390400-101393800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:101390400-101393800	Weak transcription	Thymus	Thymus
46	chr3:101390400-101394400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:101390400-101394400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:101390600-101393600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:101390600-101393600	Weak transcription	HMEC	breast
50	chr3:101390600-101393800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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