Variant report

Variant	rs7642171
Chromosome Location	chr3:119891781-119891782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119811496..119816423-chr3:119884642..119891818,9	MCF-7	breast:
2	chr3:119888337..119890858-chr3:119891647..119894832,5	MCF-7	breast:
3	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10049256	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085620	0.86[ASN][1000 genomes]
rs1085622	0.86[ASN][1000 genomes]
rs1085624	0.86[ASN][1000 genomes]
rs10934512	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934514	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934515	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934516	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934517	0.85[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707711	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11915552	0.83[ASN][1000 genomes]
rs12152218	0.86[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314898	0.81[ASN][1000 genomes]
rs1352458	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388755	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1488761	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488762	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1488764	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492271	0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1907681	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007756	0.90[EUR][1000 genomes]
rs2014133	0.85[AFR][1000 genomes]
rs2035671	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035672	0.87[EUR][1000 genomes]
rs2035673	0.87[EUR][1000 genomes]
rs2035674	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2130000	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130001	0.86[EUR][1000 genomes]
rs2131174	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171598	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171599	0.87[EUR][1000 genomes]
rs2319541	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319542	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319543	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28398784	0.84[EUR][1000 genomes]
rs2874022	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2874023	0.86[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943755	0.81[ASN][1000 genomes]
rs2971211	0.81[ASN][1000 genomes]
rs2971213	0.86[ASN][1000 genomes]
rs3112282	0.84[EUR][1000 genomes]
rs3112283	0.84[EUR][1000 genomes]
rs334539	0.86[CEU][hapmap]
rs334545	0.86[CEU][hapmap]
rs334549	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4263318	0.86[ASN][1000 genomes]
rs4314205	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4488869	0.86[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4676804	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4676809	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676822	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676832	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438558	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6438559	0.86[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438561	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6438562	0.93[EUR][1000 genomes]
rs6438564	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6438566	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438567	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764549	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769988	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772226	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775625	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776122	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777971	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781470	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6782570	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6787458	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794478	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6803611	0.94[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805050	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637828	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641838	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644268	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7653263	0.86[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653396	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787185	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs787211	0.86[ASN][1000 genomes]
rs796824	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs813697	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs814182	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs901920	0.86[EUR][1000 genomes]
rs902790	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902791	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902792	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902794	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902795	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923380	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs923726	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923727	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923728	0.86[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289142	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289143	0.86[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979682	0.86[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811483	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813834	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842302	0.86[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849023	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853082	0.86[CEU][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857123	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858566	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868058	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868312	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872165	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9881717	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119884800-119895600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
5	chr3:119886200-119892400	Strong transcription	Fetal Brain Female	brain
6	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:119888400-119892600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
11	chr3:119888600-119892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119888600-119892600	Enhancers	Osteobl	bone
13	chr3:119888600-119893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:119889400-119893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:119890000-119892000	Weak transcription	HSMM	muscle
17	chr3:119890000-119893000	Weak transcription	A549	lung
18	chr3:119890000-119895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:119890200-119892200	Strong transcription	Fetal Stomach	stomach
20	chr3:119890400-119892000	Weak transcription	HSMMtube	muscle
21	chr3:119890400-119893600	Weak transcription	Placenta	Placenta
22	chr3:119890400-119895400	Weak transcription	Psoas Muscle	Psoas
23	chr3:119890400-119895800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:119890400-119895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:119890600-119892200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:119890600-119893600	Weak transcription	Hela-S3	cervix
27	chr3:119890600-119895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:119890600-119895800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:119890800-119895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:119890800-119896000	Weak transcription	Right Atrium	heart
31	chr3:119891000-119895800	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:119891200-119892000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:119891200-119893200	Weak transcription	HMEC	breast
34	chr3:119891200-119895600	Weak transcription	Adipose Nuclei	Adipose
35	chr3:119891200-119895600	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:119891400-119895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:119891400-119895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:119891400-119895600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:119891400-119895600	Weak transcription	NHLF	lung
40	chr3:119891400-119896200	Weak transcription	Lung	lung
41	chr3:119891600-119892000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:119891600-119892200	ZNF genes & repeats	NHEK	skin

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