Variant report

Variant	rs9878606
Chromosome Location	chr3:24633038-24633039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24567024..24569936-chr3:24632741..24634847,2	K562	blood:
2	chr3:24536512..24538527-chr3:24630331..24633060,2	MCF-7	breast:
3	chr3:24631935..24633898-chr3:24636048..24638829,2	MCF-7	breast:
4	chr3:24535097..24538455-chr3:24631744..24636761,7	MCF-7	breast:
5	chr3:24350162..24351776-chr3:24632242..24634979,2	MCF-7	breast:
6	chr3:24599960..24602220-chr3:24631656..24634494,2	K562	blood:
7	chr3:24631555..24633388-chr8:96154726..96156328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10212332	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10490837	0.81[ASN][1000 genomes]
rs11712286	0.86[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13318800	0.85[ASN][1000 genomes]
rs1561079	0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs17014900	0.81[ASN][1000 genomes]
rs17014902	0.81[ASN][1000 genomes]
rs1992040	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1992041	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043578	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs2117873	0.86[ASN][1000 genomes]
rs2196434	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196438	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs28562279	0.93[ASN][1000 genomes]
rs3919672	0.82[JPT][hapmap]
rs56268655	0.85[ASN][1000 genomes]
rs58152527	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61701305	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550878	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6550879	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767534	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767717	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769209	0.95[ASN][1000 genomes]
rs6770518	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771818	0.95[ASN][1000 genomes]
rs6781066	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795607	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6801494	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73040438	0.86[ASN][1000 genomes]
rs7647700	0.85[ASN][1000 genomes]
rs930317	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310745	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9819865	0.85[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823545	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9830859	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835497	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9838616	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9838720	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9843609	0.83[ASN][1000 genomes]
rs9844544	0.84[ASN][1000 genomes]
rs9850781	0.85[ASN][1000 genomes]
rs9859978	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861129	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9868375	0.84[CHB][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9873830	0.83[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24621200-24633400	Weak transcription	K562	blood
2	chr3:24629600-24633600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:24629800-24633200	Enhancers	Fetal Lung	lung
4	chr3:24630800-24634200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:24630800-24640800	Weak transcription	Small Intestine	intestine
6	chr3:24631200-24636000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:24631400-24634600	Enhancers	HMEC	breast
8	chr3:24631400-24635200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:24631600-24633400	Enhancers	NHEK	skin
10	chr3:24631600-24634200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:24631600-24634200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:24631600-24634400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:24631600-24634400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:24631800-24634600	Enhancers	Fetal Intestine Large	intestine
15	chr3:24632000-24633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:24632000-24636200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:24632000-24637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:24632000-24640000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:24632200-24635800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:24632200-24637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:24632600-24633800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:24632600-24634200	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr3:24632600-24634600	Enhancers	Fetal Intestine Small	intestine
24	chr3:24632800-24633200	Weak transcription	HUVEC	blood vessel
25	chr3:24632800-24633600	Enhancers	Stomach Mucosa	stomach
26	chr3:24632800-24633600	Enhancers	NHDF-Ad	bronchial
27	chr3:24632800-24633800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:24632800-24634600	Enhancers	Primary hematopoietic stem cells	blood
29	chr3:24633000-24633600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:24633000-24633600	Enhancers	HSMM	muscle
31	chr3:24633000-24633800	Enhancers	Fetal Brain Male	brain
32	chr3:24633000-24633800	Enhancers	Placenta	Placenta
33	chr3:24633000-24633800	Enhancers	A549	lung
34	chr3:24633000-24634400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:24633000-24634600	Enhancers	Hela-S3	cervix

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