Variant report

Variant	rs6438561
Chromosome Location	chr3:119870034-119870035
allele	A/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	chr3:119867871..119870349-chr3:119875712..119877295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10049256	0.90[EUR][1000 genomes]
rs10934512	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10934514	0.85[EUR][1000 genomes]
rs10934515	0.90[EUR][1000 genomes]
rs10934516	0.90[EUR][1000 genomes]
rs10934517	0.90[EUR][1000 genomes]
rs11707711	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12152218	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1352458	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1488761	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1488762	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1488764	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1907681	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2007756	0.85[EUR][1000 genomes]
rs2014133	0.83[AFR][1000 genomes]
rs2035671	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2035672	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2035673	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2035674	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2130000	0.90[EUR][1000 genomes]
rs2130001	0.82[EUR][1000 genomes]
rs2131174	0.82[EUR][1000 genomes]
rs2171598	0.90[EUR][1000 genomes]
rs2171599	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2319541	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2319542	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2319543	0.90[EUR][1000 genomes]
rs28398784	0.80[EUR][1000 genomes]
rs2874022	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2874023	0.90[EUR][1000 genomes]
rs4488869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4676804	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4676809	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4676822	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4676832	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6438559	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438562	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6438564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6438566	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438567	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6764549	0.90[EUR][1000 genomes]
rs6769988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775625	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6776122	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6777971	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6781470	0.80[EUR][1000 genomes]
rs6782570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6794478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6805050	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7637828	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7641838	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7642171	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7653263	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653396	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs901920	0.82[EUR][1000 genomes]
rs902790	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902791	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902792	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs902794	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs902795	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923380	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs923726	0.90[EUR][1000 genomes]
rs923727	0.90[EUR][1000 genomes]
rs923728	0.90[EUR][1000 genomes]
rs9289142	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9289143	0.90[EUR][1000 genomes]
rs979682	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9813834	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9841122	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9842302	0.90[EUR][1000 genomes]
rs9849023	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9853082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9857123	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9858566	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9868058	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9868312	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9872165	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9881717	0.91[AFR][1000 genomes];0.93[AMR][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119864600-119871800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:119864800-119871600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:119865000-119870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:119865000-119870800	Weak transcription	Osteobl	bone
5	chr3:119865200-119870200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119866600-119870800	Weak transcription	NHDF-Ad	bronchial
7	chr3:119866600-119871400	Weak transcription	Lung	lung
8	chr3:119866800-119871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:119867000-119870800	Weak transcription	Stomach Mucosa	stomach
10	chr3:119867000-119872000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:119867200-119871800	Enhancers	NHEK	skin
12	chr3:119867200-119872000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:119867200-119873400	Weak transcription	HSMMtube	muscle
14	chr3:119867600-119871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:119867600-119871400	Weak transcription	Spleen	Spleen
16	chr3:119867600-119872000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:119867800-119870200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:119867800-119870400	Weak transcription	HepG2	liver
19	chr3:119867800-119870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:119867800-119870800	Weak transcription	Placenta	Placenta
21	chr3:119867800-119870800	Weak transcription	Hela-S3	cervix
22	chr3:119867800-119870800	Weak transcription	HUVEC	blood vessel
23	chr3:119867800-119871000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:119867800-119871800	Weak transcription	Adipose Nuclei	Adipose
25	chr3:119867800-119871800	Weak transcription	Left Ventricle	heart
26	chr3:119868000-119870200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:119868000-119870400	Weak transcription	HMEC	breast
28	chr3:119868400-119870600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:119869400-119870200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:119869400-119871200	Enhancers	Fetal Intestine Small	intestine

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