Variant report

Variant	rs10885575
Chromosome Location	chr10:116297297-116297298
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	chr10:116296905..116298827-chr10:116577093..116580051,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10749169	0.85[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs10749170	0.85[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs10885572	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885573	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885580	0.81[ASN][1000 genomes]
rs11196779	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196785	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12569428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145894	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247528	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247624	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2475239	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2475240	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2475241	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2475242	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483531	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483564	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2483567	0.82[TSI][hapmap]
rs2483571	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483577	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2483579	0.86[EUR][1000 genomes]
rs2483580	0.91[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2483584	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2483585	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483587	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483588	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483596	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483599	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483612	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497708	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2497710	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2497712	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2497717	0.80[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497718	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497720	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2497721	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2497722	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2497723	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35078486	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144582	0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs4514325	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56001223	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56086836	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339171	0.82[ASN][1000 genomes]
rs7094292	0.83[AMR][1000 genomes]
rs867736	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883511	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883768	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914938	0.90[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9421179	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10885575	ABLIM1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116286800-116298000	Weak transcription	Esophagus	oesophagus
2	chr10:116287000-116298200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:116287000-116298200	Weak transcription	Lung	lung
4	chr10:116287000-116301200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:116287200-116299400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr10:116287200-116299400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:116287200-116300600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:116287200-116301600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:116287200-116307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:116287400-116297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:116287400-116297400	Weak transcription	Fetal Heart	heart
12	chr10:116287400-116297600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:116287400-116297800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:116287400-116298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:116287400-116298000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:116287400-116298200	Weak transcription	HMEC	breast
17	chr10:116287400-116300400	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:116287400-116300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:116287400-116300600	Weak transcription	Colon Smooth Muscle	Colon
20	chr10:116287400-116300800	Weak transcription	Fetal Intestine Large	intestine
21	chr10:116287400-116303200	Weak transcription	Brain Anterior Caudate	brain
22	chr10:116287400-116303800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:116287400-116310600	Weak transcription	Brain Angular Gyrus	brain
24	chr10:116287400-116310600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:116287600-116298000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:116287600-116298000	Weak transcription	Fetal Muscle Leg	muscle
27	chr10:116288800-116298000	Weak transcription	Right Ventricle	heart
28	chr10:116292400-116298000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr10:116292400-116303800	Weak transcription	Pancreas	Pancrea
30	chr10:116292600-116297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:116292600-116297800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:116292600-116298000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr10:116294000-116298000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr10:116294000-116300800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr10:116294200-116298200	Weak transcription	Spleen	Spleen
36	chr10:116294400-116300200	Weak transcription	Placenta	Placenta
37	chr10:116294600-116297800	Weak transcription	Stomach Mucosa	stomach
38	chr10:116295000-116297400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:116295000-116297800	Weak transcription	Fetal Lung	lung
40	chr10:116295200-116297800	Weak transcription	HUVEC	blood vessel
41	chr10:116295200-116298000	Weak transcription	Ovary	ovary
42	chr10:116295600-116298000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr10:116295800-116298000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:116296200-116298200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr10:116296200-116298200	Enhancers	Thymus	Thymus
46	chr10:116296400-116297600	Enhancers	Primary T cells from cord blood	blood
47	chr10:116296600-116297400	Strong transcription	HSMM	muscle
48	chr10:116296600-116297800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr10:116296600-116298000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr10:116296600-116298000	Enhancers	Primary T helper cells fromperipheralblood	blood

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