Variant report

Variant	rs3798456
Chromosome Location	chr6:76481997-76481998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:76469142..76471151-chr6:76480358..76482124,2	MCF-7	breast:
2	chr6:76472032..76473906-chr6:76480774..76483408,2	MCF-7	breast:
3	chr6:76310227..76312452-chr6:76481370..76483085,2	K562	blood:

Variant related genes	Relation type
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 127 )
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];0.85[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[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]
rs3798453	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];0.81[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:24 , 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	nsv1023331	chr6:76238459-76482117	Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv538315	chr6:76238459-76482117	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	nsv1023749	chr6:76287578-76482117	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv538317	chr6:76287578-76482117	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	nsv970689	chr6:76481616-76485006	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76461000-76485000	Weak transcription	Fetal Stomach	stomach
2	chr6:76461600-76485000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:76462400-76482200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:76463400-76485200	Weak transcription	Gastric	stomach
5	chr6:76464200-76485000	Weak transcription	Pancreas	Pancrea
6	chr6:76469400-76484800	Weak transcription	Left Ventricle	heart
7	chr6:76469400-76485200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:76470000-76485000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:76470200-76483200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:76470800-76486400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:76472400-76485000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:76472600-76484600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:76472600-76528000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:76474000-76483000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:76474600-76491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:76477400-76485000	Weak transcription	Lung	lung
17	chr6:76478800-76482000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:76479600-76488200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:76480800-76482200	Weak transcription	Brain Angular Gyrus	brain
20	chr6:76480800-76482400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:76480800-76491000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:76481600-76482600	Enhancers	HUVEC	blood vessel
23	chr6:76481800-76483600	Enhancers	Brain Hippocampus Middle	brain
24	chr6:76481800-76483600	Enhancers	Brain Inferior Temporal Lobe	brain

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