Variant report

Variant	rs3798453
Chromosome Location	chr6:76485518-76485519
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	chr6:76458193..76461486-chr6:76482230..76486067,4	MCF-7	breast:
2	chr6:76459866..76461619-chr6:76483545..76486040,2	K562	blood:

Variant related genes	Relation type
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11963710	0.95[ASN][1000 genomes]
rs11964201	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11965869	1.00[CEU][hapmap]
rs11967411	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11968058	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11968226	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11969264	0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12660075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12660330	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12660493	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12661973	0.91[ASN][1000 genomes]
rs12662248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662565	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662672	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662718	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12662824	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662879	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12663203	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663535	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12664146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12664721	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12664742	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665404	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13205059	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498383	1.00[CEU][hapmap]
rs16879451	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886792	1.00[CEU][hapmap]
rs16886870	1.00[CEU][hapmap]
rs2273858	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2295937	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs3778009	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798436	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798445	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3798450	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798451	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56251027	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59710688	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60360183	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61620194	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67182025	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654750	0.82[ASN][1000 genomes]
rs72654751	0.91[ASN][1000 genomes]
rs72654752	0.94[ASN][1000 genomes]
rs72654753	0.96[ASN][1000 genomes]
rs72654754	0.96[ASN][1000 genomes]
rs72654755	0.95[ASN][1000 genomes]
rs72654756	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654757	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654758	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654759	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654760	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654761	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654762	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654763	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654764	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654765	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654766	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654767	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654769	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654770	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654771	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654772	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654773	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654774	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654775	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654776	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654777	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654778	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654779	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654780	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72654781	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654783	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654784	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654785	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654786	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654787	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72654788	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72654789	0.80[EUR][1000 genomes]
rs72654790	0.80[EUR][1000 genomes]
rs72654791	0.80[EUR][1000 genomes]
rs72654792	0.80[EUR][1000 genomes]
rs72654793	0.80[EUR][1000 genomes]
rs72674543	0.80[EUR][1000 genomes]
rs72674544	0.80[EUR][1000 genomes]
rs72674546	0.80[EUR][1000 genomes]
rs73751021	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73751022	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73751024	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761217	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9443187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9443191	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9443192	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9447543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9447544	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9447545	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9447546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447549	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447552	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447555	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
5	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv1017542	chr6:76238459-76537447	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1031745	chr6:76257913-76493355	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv538316	chr6:76257913-76493355	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv533100	chr6:76257914-76493354	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv886185	chr6:76320846-76498109	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
19	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76470800-76486400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:76472600-76528000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:76474600-76491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:76479600-76488200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:76480800-76491000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:76482400-76486800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:76482600-76491000	Weak transcription	HUVEC	blood vessel
8	chr6:76484800-76485600	Enhancers	Brain Anterior Caudate	brain
9	chr6:76484800-76485600	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:76484800-76485600	Enhancers	Brain Hippocampus Middle	brain
11	chr6:76484800-76485600	Enhancers	Brain Substantia Nigra	brain
12	chr6:76484800-76485800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:76484800-76485800	Enhancers	Fetal Heart	heart
14	chr6:76484800-76486600	Enhancers	K562	blood
15	chr6:76485000-76485600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:76485200-76485800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:76485400-76488800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:76485400-76490800	Weak transcription	Fetal Intestine Large	intestine
19	chr6:76485400-76491000	Weak transcription	NHLF	lung
20	chr6:76485400-76491200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:76485400-76491200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:76485400-76491400	Weak transcription	Pancreas	Pancrea
23	chr6:76485400-76491600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:76485400-76492400	Weak transcription	Fetal Stomach	stomach
25	chr6:76485400-76501600	Weak transcription	Left Ventricle	heart
26	chr6:76485400-76502200	Weak transcription	Brain Angular Gyrus	brain
27	chr6:76485400-76523000	Weak transcription	Lung	lung

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