Variant report

Variant	rs17387244
Chromosome Location	chr10:91217902-91217903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr10:91217841-91218567	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000234452	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11203135	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11203136	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11593758	0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11594380	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11596684	0.86[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331147	1.00[YRI][hapmap]
rs17122097	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs17122257	0.84[CHB][hapmap]
rs17122305	0.84[CHB][hapmap]
rs3740029	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59542683	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17387244	ACTA2	cis	parietal	SCAN
rs17387244	PTEN	cis	cerebellum	SCAN
rs17387244	TNKS2	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91179600-91225600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:91198800-91223600	Weak transcription	Left Ventricle	heart
3	chr10:91214000-91223600	Weak transcription	Pancreas	Pancrea
4	chr10:91214200-91223400	Weak transcription	Placenta	Placenta
5	chr10:91217200-91218200	Enhancers	HUVEC	blood vessel
6	chr10:91217400-91218000	Enhancers	NHEK	skin
7	chr10:91217400-91219200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:91217400-91219200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:91217600-91218000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:91217600-91218000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr10:91217600-91218000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:91217600-91218000	Enhancers	NHLF	lung
13	chr10:91217600-91218200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:91217600-91218200	Enhancers	Osteobl	bone
15	chr10:91217600-91218400	Enhancers	Fetal Lung	lung
16	chr10:91217600-91218600	Enhancers	NHDF-Ad	bronchial
17	chr10:91217600-91218800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:91217600-91219000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:91217600-91219000	Enhancers	HMEC	breast
20	chr10:91217600-91219000	Enhancers	HSMM	muscle
21	chr10:91217600-91219200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:91217600-91219400	Enhancers	Fetal Heart	heart
23	chr10:91217600-91219400	Enhancers	Hela-S3	cervix
24	chr10:91217600-91220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:91217800-91218000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:91217800-91218200	Enhancers	NH-A	brain
27	chr10:91217800-91218800	Enhancers	HSMMtube	muscle
28	chr10:91217800-91219000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:91217800-91219200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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