Variant report

Variant	rs10882474
Chromosome Location	chr10:96305729-96305730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:96120995..96123181-chr10:96304440..96307322,3	MCF-7	breast:
2	chr10:96160448..96164371-chr10:96304138..96307716,8	MCF-7	breast:
3	chr10:96304740..96307263-chr10:96312412..96314149,2	MCF-7	breast:
4	chr10:96159758..96162488-chr10:96305268..96307065,2	K562	blood:
5	chr10:96290006..96295152-chr10:96302633..96306565,5	K562	blood:
6	chr10:96305623..96306527-chr6:64282239..64282872,2	Hela-S3	cervix:
7	chr10:96305128..96305906-chr3:50336255..50337029,2	Hela-S3	cervix:
8	chr10:96305041..96305800-chr22:46465255..46466051,2	Hela-S3	cervix:
9	chr10:96305075..96307344-chr10:96312057..96315359,3	K562	blood:
10	chr10:96304986..96305759-chr17:8076339..8077014,2	Hela-S3	cervix:
11	chr10:96305307..96305951-chr16:2058934..2059919,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000243477	Chromatin interaction
ENSG00000173145	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000108239	Chromatin interaction
ENSG00000167962	Chromatin interaction
ENSG00000266680	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000119969	Chromatin interaction
ENSG00000235159	Chromatin interaction
ENSG00000186792	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10786168	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10786170	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10882454	0.82[EUR][1000 genomes]
rs10882460	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs10882463	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs10882469	0.88[EUR][1000 genomes]
rs10882470	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs10882471	0.90[EUR][1000 genomes]
rs10882473	0.89[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882481	0.83[EUR][1000 genomes]
rs10882486	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187937	0.84[EUR][1000 genomes]
rs11187939	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11187940	0.92[JPT][hapmap]
rs11187944	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11187948	0.91[MEX][hapmap];0.84[TSI][hapmap]
rs11187952	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11187960	1.00[JPT][hapmap]
rs11187972	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11187973	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11187980	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs11187996	0.88[EUR][1000 genomes]
rs11188009	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188012	0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs11188015	0.84[EUR][1000 genomes]
rs11188016	0.86[EUR][1000 genomes]
rs11188017	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11188019	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11188020	1.00[JPT][hapmap]
rs11188026	0.87[EUR][1000 genomes]
rs11188030	0.87[EUR][1000 genomes]
rs11188038	0.84[EUR][1000 genomes]
rs11188039	0.83[EUR][1000 genomes]
rs11188040	0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs11188041	0.83[EUR][1000 genomes]
rs11527881	0.86[EUR][1000 genomes]
rs11592354	0.88[EUR][1000 genomes]
rs11638	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12218213	0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12218216	0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12219906	0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12220588	0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12221475	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs12572040	0.90[EUR][1000 genomes]
rs12762574	0.86[EUR][1000 genomes]
rs1326839	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334595	1.00[JPT][hapmap]
rs1359262	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1359263	0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1409655	1.00[JPT][hapmap]
rs1749352	0.83[EUR][1000 genomes]
rs1854035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1886272	0.81[EUR][1000 genomes]
rs1889485	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1889486	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1931757	0.83[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1977288	1.00[JPT][hapmap]
rs1977289	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1977290	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1977291	0.83[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs2012670	0.82[EUR][1000 genomes]
rs2095380	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2148553	0.82[EUR][1000 genomes]
rs2265364	0.84[EUR][1000 genomes]
rs2274096	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274417	0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2281791	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2860821	0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2860840	1.00[JPT][hapmap]
rs2901765	0.83[EUR][1000 genomes]
rs34814196	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3740358	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758522	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758523	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3781262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4351744	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs4421688	0.87[EUR][1000 genomes]
rs480032	1.00[JPT][hapmap]
rs4918333	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4918401	0.86[EUR][1000 genomes]
rs4918402	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4918403	0.84[EUR][1000 genomes]
rs4918404	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4918411	0.84[EUR][1000 genomes]
rs4918412	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4918417	0.83[EUR][1000 genomes]
rs4918418	0.84[EUR][1000 genomes]
rs4918419	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs556055	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6583942	1.00[JPT][hapmap]
rs6583943	0.85[EUR][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs6583945	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6583946	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68046102	0.83[EUR][1000 genomes]
rs692872	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs701885	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7068337	0.85[EUR][1000 genomes]
rs7073639	0.83[EUR][1000 genomes]
rs7075182	0.88[JPT][hapmap]
rs7078236	0.87[EUR][1000 genomes]
rs7078478	0.83[JPT][hapmap]
rs7078811	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7079934	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs7087798	0.83[JPT][hapmap]
rs7089094	0.82[EUR][1000 genomes]
rs7092129	1.00[JPT][hapmap]
rs7100415	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7898330	0.81[EUR][1000 genomes]
rs7906843	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7906968	0.83[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7921721	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs912466	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9420641	0.83[EUR][1000 genomes]
rs9633699	0.84[EUR][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10882474	HELLS	cis	cerebellum	SCAN
rs10882474	C19orf22	trans	cerebellum	SCAN
rs10882474	FGFBP3	cis	cerebellum	SCAN
rs10882474	KIF11	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96304200-96306200	Active TSS	Colonic Mucosa	Colon
2	chr10:96304200-96306400	Active TSS	HSMM	muscle
3	chr10:96304200-96306800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:96304200-96306800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:96304200-96307000	Active TSS	A549	lung
6	chr10:96304400-96305800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr10:96304400-96305800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr10:96304400-96306000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:96304400-96306200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr10:96304400-96306200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:96304400-96306200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:96304400-96306200	Active TSS	HMEC	breast
13	chr10:96304400-96306200	Active TSS	NH-A	brain
14	chr10:96304400-96306400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr10:96304400-96306400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr10:96304400-96306400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr10:96304400-96306600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:96304400-96306600	Active TSS	NHDF-Ad	bronchial
19	chr10:96304400-96306800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:96304400-96306800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:96304400-96306800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:96304400-96307000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:96304400-96307000	Active TSS	Muscle Satellite Cultured Cells	--
24	chr10:96304400-96307200	Active TSS	GM12878-XiMat	blood
25	chr10:96304400-96307400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr10:96304400-96307400	Active TSS	K562	blood
27	chr10:96304400-96307600	Active TSS	NHLF	lung
28	chr10:96304400-96309000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:96304600-96306000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:96304600-96306000	Active TSS	Brain Anterior Caudate	brain
31	chr10:96304600-96306000	Active TSS	Brain Cingulate Gyrus	brain
32	chr10:96304600-96306000	Active TSS	Colon Smooth Muscle	Colon
33	chr10:96304600-96306200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr10:96304600-96306200	Active TSS	Aorta	Aorta
35	chr10:96304600-96306200	Active TSS	Ovary	ovary
36	chr10:96304600-96306200	Active TSS	Psoas Muscle	Psoas
37	chr10:96304600-96306400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:96304600-96306400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr10:96304600-96306400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr10:96304600-96306400	Active TSS	Fetal Brain Female	brain
41	chr10:96304600-96306400	Active TSS	Fetal Heart	heart
42	chr10:96304600-96306400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr10:96304600-96306400	Active TSS	Fetal Lung	lung
44	chr10:96304600-96306400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr10:96304600-96306400	Active TSS	Right Atrium	heart
46	chr10:96304600-96306400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr10:96304600-96306600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:96304600-96306600	Active TSS	Fetal Intestine Large	intestine
49	chr10:96304600-96306600	Active TSS	HSMMtube	muscle
50	chr10:96304600-96306600	Active TSS	NHEK	skin

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