Variant report

Variant	rs10490837
Chromosome Location	chr3:24632124-24632125
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24536512..24538527-chr3:24630331..24633060,2	MCF-7	breast:
2	chr3:24561637..24564260-chr3:24630059..24632291,3	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	chr3:24599960..24602220-chr3:24631656..24634494,2	K562	blood:
6	chr3:24631555..24633388-chr8:96154726..96156328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000265028	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10212332	0.80[ASN][1000 genomes]
rs11708042	0.83[EUR][1000 genomes]
rs11712286	0.85[CHB][hapmap]
rs11715809	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12489628	1.00[YRI][hapmap]
rs13318800	0.84[EUR][1000 genomes]
rs17014900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992040	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs2043579	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2117873	0.84[EUR][1000 genomes]
rs2117874	0.85[EUR][1000 genomes]
rs2196434	0.81[ASN][1000 genomes]
rs2196435	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2196438	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs28562279	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3919672	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs55720954	0.89[AFR][1000 genomes]
rs56135387	0.93[EUR][1000 genomes]
rs56268655	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56281969	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs58152527	0.80[ASN][1000 genomes]
rs61701305	0.80[ASN][1000 genomes]
rs6550879	0.93[CHB][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs6767717	0.81[ASN][1000 genomes]
rs6769209	0.84[EUR][1000 genomes]
rs6771818	0.84[EUR][1000 genomes]
rs6795607	0.93[CHB][hapmap];0.84[MEX][hapmap]
rs6801494	0.81[ASN][1000 genomes]
rs73036499	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73036501	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73038411	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73038427	0.96[EUR][1000 genomes]
rs73040431	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73040438	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73040440	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73040465	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs73040478	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs73040479	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7647700	0.84[EUR][1000 genomes]
rs930317	0.81[ASN][1000 genomes]
rs9310745	0.93[CHB][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs9819865	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs9823545	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs9830859	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9835497	0.93[CHB][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs9838616	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs9838720	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs9843609	0.84[EUR][1000 genomes]
rs9844544	0.84[EUR][1000 genomes]
rs9850781	0.84[EUR][1000 genomes]
rs9853927	0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs9861129	0.85[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes]
rs9868375	1.00[CHB][hapmap]
rs9873830	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9878606	0.81[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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24621200-24633400	Weak transcription	K562	blood
2	chr3:24628800-24633000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:24629600-24632200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:24629600-24633600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr3:24629800-24633200	Enhancers	Fetal Lung	lung
6	chr3:24630600-24632800	Weak transcription	Stomach Mucosa	stomach
7	chr3:24630800-24634200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:24630800-24640800	Weak transcription	Small Intestine	intestine
9	chr3:24631000-24632800	Enhancers	HUVEC	blood vessel
10	chr3:24631200-24636000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:24631400-24632400	Enhancers	NHDF-Ad	bronchial
12	chr3:24631400-24634600	Enhancers	HMEC	breast
13	chr3:24631400-24635200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:24631600-24632200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:24631600-24633400	Enhancers	NHEK	skin
16	chr3:24631600-24634200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:24631600-24634200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:24631600-24634400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:24631600-24634400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:24631800-24632200	Enhancers	Fetal Brain Male	brain
21	chr3:24631800-24632200	Enhancers	Fetal Intestine Small	intestine
22	chr3:24631800-24632600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:24631800-24634600	Enhancers	Fetal Intestine Large	intestine
24	chr3:24632000-24632200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:24632000-24632800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:24632000-24633000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:24632000-24633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:24632000-24636200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:24632000-24637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:24632000-24640000	Weak transcription	Duodenum Mucosa	Duodenum

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