Variant report

Variant	rs2035674
Chromosome Location	chr3:119862702-119862703
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119811328..119819569-chr3:119859303..119870611,43	MCF-7	breast:
2	chr3:119809272..119819238-chr3:119861129..119869186,35	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10049256	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10934512	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs10934514	0.84[EUR][1000 genomes]
rs10934515	0.89[EUR][1000 genomes]
rs10934516	0.89[EUR][1000 genomes]
rs10934517	0.89[EUR][1000 genomes]
rs1154596	0.87[CEU][hapmap]
rs1154597	0.87[CEU][hapmap]
rs11707711	0.89[EUR][1000 genomes]
rs12152218	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13312998	0.87[CEU][hapmap]
rs1352458	0.89[EUR][1000 genomes]
rs1488761	0.89[EUR][1000 genomes]
rs1488762	0.89[EUR][1000 genomes]
rs1488764	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1492271	0.87[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs16830683	0.87[CEU][hapmap]
rs182839	0.87[CEU][hapmap]
rs1907681	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2035671	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2035672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2046954	0.80[AMR][1000 genomes]
rs2130000	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2130001	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2131174	0.82[EUR][1000 genomes]
rs2171598	0.89[EUR][1000 genomes]
rs2171599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319541	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2319542	0.89[EUR][1000 genomes]
rs2319543	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28398784	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2874022	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2874023	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3112282	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3112283	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334534	0.87[CEU][hapmap]
rs334539	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs334540	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs334545	1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[AMR][1000 genomes]
rs334549	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs334561	0.87[CEU][hapmap]
rs4488869	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4676804	0.89[EUR][1000 genomes]
rs4676809	0.89[EUR][1000 genomes]
rs4676822	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4676832	0.82[EUR][1000 genomes]
rs6438554	0.87[CEU][hapmap]
rs6438558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438559	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438561	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6438562	0.88[EUR][1000 genomes]
rs6438564	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438566	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438567	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6764549	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6769988	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6775625	0.83[EUR][1000 genomes]
rs6776122	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6777971	0.82[EUR][1000 genomes]
rs6781470	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782570	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6784239	0.87[CEU][hapmap]
rs6785050	0.87[CEU][hapmap]
rs6794478	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6797689	0.87[CEU][hapmap]
rs6803611	0.87[CEU][hapmap]
rs6805050	0.89[EUR][1000 genomes]
rs7637828	0.89[EUR][1000 genomes]
rs7641838	0.89[EUR][1000 genomes]
rs7642171	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs7644268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7650554	0.87[CEU][hapmap]
rs7653263	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7653396	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs787211	0.87[CEU][hapmap]
rs901920	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902790	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs902791	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs902792	0.89[EUR][1000 genomes]
rs902794	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs902795	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs923380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923726	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs923727	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs923728	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9289142	0.89[EUR][1000 genomes]
rs9289143	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs979682	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9813834	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9841122	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9841303	1.00[CHB][hapmap]
rs9842302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9849023	0.84[EUR][1000 genomes]
rs9853082	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9857123	0.89[EUR][1000 genomes]
rs9858566	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9868058	0.86[EUR][1000 genomes]
rs9868312	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119844200-119863400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119854400-119863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119854600-119863000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:119860800-119864400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:119861200-119866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:119861400-119863000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:119861400-119863000	Weak transcription	HSMMtube	muscle
8	chr3:119861400-119863200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:119861400-119863200	Weak transcription	Osteobl	bone
10	chr3:119861600-119863000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:119862000-119867800	Enhancers	Placenta	Placenta
12	chr3:119862200-119866400	Enhancers	HepG2	liver
13	chr3:119862400-119863400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119862400-119865200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:119862600-119863200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:119862600-119863200	Enhancers	Hela-S3	cervix
17	chr3:119862600-119864200	Enhancers	A549	lung
18	chr3:119862600-119864800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:119862600-119864800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:119862600-119865000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:119862600-119868000	Enhancers	HMEC	breast

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