Variant report

Variant	rs11196828
Chromosome Location	chr10:116408015-116408016
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	chr10:116406281..116408258-chr10:116409177..116411932,2	MCF-7	breast:
2	chr10:116406490..116408753-chr10:116411218..116414182,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10787544	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10885589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885590	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1109267	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];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196807	0.89[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11196819	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11196835	0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11196843	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs11593135	0.89[YRI][hapmap]
rs11597188	0.80[GIH][hapmap];0.89[YRI][hapmap]
rs12220330	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12570718	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12776647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333681	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17719089	0.87[ASW][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17719358	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35505004	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4568917	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4606401	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4752043	0.81[AMR][1000 genomes]
rs4752099	0.80[GIH][hapmap]
rs7904491	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11196828	ABLIM1	cis	parietal	SCAN
rs11196828	TCF7L2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116394400-116422600	Weak transcription	Fetal Intestine Small	intestine
2	chr10:116395800-116408400	Weak transcription	Psoas Muscle	Psoas
3	chr10:116396200-116408800	Weak transcription	Esophagus	oesophagus
4	chr10:116397200-116409400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:116399200-116410400	Weak transcription	Brain Angular Gyrus	brain
6	chr10:116399600-116408600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:116399800-116413800	Weak transcription	Spleen	Spleen
8	chr10:116400200-116408600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:116402000-116408400	Weak transcription	Right Ventricle	heart
10	chr10:116403200-116412200	Weak transcription	Brain Anterior Caudate	brain
11	chr10:116404400-116409400	Weak transcription	Gastric	stomach
12	chr10:116404400-116411000	Enhancers	Fetal Heart	heart
13	chr10:116404600-116411200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr10:116404800-116409600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr10:116404800-116412200	Weak transcription	Lung	lung
16	chr10:116405000-116409400	Weak transcription	Pancreas	Pancrea
17	chr10:116405200-116413400	Weak transcription	Colonic Mucosa	Colon
18	chr10:116405800-116408200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr10:116406200-116412800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:116406200-116422000	Weak transcription	Fetal Lung	lung
21	chr10:116406800-116410200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:116407000-116408600	Enhancers	Osteobl	bone
23	chr10:116407000-116408800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:116407000-116408800	Enhancers	NH-A	brain
25	chr10:116407000-116409000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:116407000-116409000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr10:116407000-116409600	Enhancers	HMEC	breast
28	chr10:116407000-116409800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:116407000-116410400	Enhancers	HSMM	muscle
30	chr10:116407200-116408400	Weak transcription	Placenta	Placenta
31	chr10:116407200-116408600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr10:116407200-116408600	Enhancers	K562	blood
33	chr10:116407200-116409000	Enhancers	NHLF	lung
34	chr10:116407200-116409400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:116407200-116409600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr10:116407200-116410200	Enhancers	Liver	Liver
37	chr10:116407200-116410200	Enhancers	HSMMtube	muscle
38	chr10:116407400-116408400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:116407400-116408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr10:116407400-116408600	Flanking Active TSS	A549	lung
41	chr10:116407400-116408800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:116407400-116410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:116407600-116409000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr10:116407800-116408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:116407800-116408200	Weak transcription	Left Ventricle	heart
46	chr10:116407800-116408600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr10:116407800-116408600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr10:116407800-116408600	Flanking Active TSS	Hela-S3	cervix
49	chr10:116407800-116408600	Enhancers	NHDF-Ad	bronchial
50	chr10:116407800-116411400	Enhancers	HepG2	liver

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