Variant report

Variant	rs4688054
Chromosome Location	chr3:119733710-119733711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119729710..119735147-chr3:119812192..119816098,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10934503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934505	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934507	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154595	0.87[JPT][hapmap]
rs11915717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11917714	0.80[ASN][1000 genomes]
rs12053912	0.82[CEU][hapmap]
rs12054090	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12108149	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12630592	0.87[JPT][hapmap]
rs12630829	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632325	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12635018	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13314595	0.89[YRI][hapmap]
rs13321783	0.87[JPT][hapmap]
rs1574154	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs16830567	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16830689	0.85[YRI][hapmap]
rs16830730	0.82[CEU][hapmap]
rs1719889	0.96[YRI][hapmap]
rs1719894	0.87[JPT][hapmap]
rs17204878	0.87[JPT][hapmap]
rs1732170	0.91[JPT][hapmap]
rs1870931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980718	0.85[ASN][1000 genomes]
rs2199503	0.82[JPT][hapmap]
rs2276707	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs2319398	0.87[JPT][hapmap]
rs2319399	0.87[JPT][hapmap]
rs28536662	0.87[JPT][hapmap]
rs2873950	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs28831519	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3107669	0.87[JPT][hapmap]
rs334533	0.87[JPT][hapmap]
rs334535	0.92[YRI][hapmap]
rs334559	0.82[YRI][hapmap]
rs334563	0.87[JPT][hapmap]
rs3732359	0.87[JPT][hapmap];0.86[TSI][hapmap]
rs3732360	0.87[JPT][hapmap]
rs3732361	0.91[JPT][hapmap]
rs3814057	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs3814058	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4072520	0.82[YRI][hapmap]
rs4261913	0.83[JPT][hapmap]
rs4340737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4624596	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4687890	0.87[JPT][hapmap]
rs4687893	0.87[JPT][hapmap]
rs4688042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4688046	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4688047	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688053	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56728675	0.83[ASN][1000 genomes]
rs57939147	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs58493895	0.83[ASN][1000 genomes]
rs58863896	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60235167	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60393216	0.83[ASN][1000 genomes]
rs62264706	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62264708	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62264714	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62264734	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62264739	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264742	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264743	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264747	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264749	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266274	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266277	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62266281	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438552	0.87[JPT][hapmap]
rs6438553	0.87[JPT][hapmap]
rs6769435	0.82[YRI][hapmap]
rs6770314	0.92[YRI][hapmap]
rs6773751	0.80[ASN][1000 genomes]
rs6775397	0.83[YRI][hapmap]
rs6781942	0.87[JPT][hapmap]
rs6782799	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6790751	0.89[YRI][hapmap]
rs6792572	0.87[JPT][hapmap]
rs6795653	0.87[JPT][hapmap]
rs6797459	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6800622	0.87[JPT][hapmap]
rs6805251	0.86[JPT][hapmap]
rs6808874	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7431209	0.86[JPT][hapmap]
rs7617372	0.89[YRI][hapmap]
rs7620750	0.89[YRI][hapmap]
rs7633279	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7639388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7644234	0.87[JPT][hapmap]
rs7652172	0.85[YRI][hapmap]
rs9813864	0.91[JPT][hapmap]
rs9851174	0.92[YRI][hapmap]
rs9873477	0.87[JPT][hapmap]
rs9878473	0.87[JPT][hapmap]
rs9879992	0.85[YRI][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
2	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
3	chr3:119718200-119736800	Weak transcription	Liver	Liver
4	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
7	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:119723200-119734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119723200-119736200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:119724000-119736800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:119724000-119738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
14	chr3:119724200-119734600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:119729800-119734000	Enhancers	Brain Substantia Nigra	brain
16	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:119730600-119733800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:119730600-119736200	Weak transcription	Stomach Mucosa	stomach
20	chr3:119730600-119736400	Weak transcription	Small Intestine	intestine
21	chr3:119730600-119739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
23	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:119730800-119736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:119731200-119736800	Weak transcription	Adipose Nuclei	Adipose
27	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:119731600-119737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:119731800-119733800	Enhancers	Brain Hippocampus Middle	brain
30	chr3:119731800-119737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:119731800-119739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:119732000-119734000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:119732000-119734200	Enhancers	HUVEC	blood vessel
34	chr3:119732000-119736200	Weak transcription	Psoas Muscle	Psoas
35	chr3:119732000-119739400	Weak transcription	Ovary	ovary
36	chr3:119732200-119734000	Enhancers	A549	lung
37	chr3:119732200-119734000	Enhancers	HepG2	liver
38	chr3:119732200-119747200	Weak transcription	Gastric	stomach
39	chr3:119732200-119747600	Weak transcription	Right Ventricle	heart
40	chr3:119732400-119734600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:119732400-119736400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:119732600-119734600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:119732600-119734800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:119732600-119734800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:119732600-119735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:119732600-119735000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:119732600-119736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:119732600-119736200	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:119732600-119736400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:119732600-119736800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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