Variant report

Variant	rs304430
Chromosome Location	chr10:91226876-91226877
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	chr10:91225996..91226933-chr10:91323304..91324280,5	MCF-7	breast:
2	chr10:91219240..91223064-chr10:91225157..91229042,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234452	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs160053	0.91[ASN][1000 genomes]
rs160054	0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs303162	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs303175	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303177	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs303178	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs303179	0.82[AMR][1000 genomes]
rs303181	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs303183	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs303184	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs303188	0.91[CEU][hapmap]
rs303190	0.85[EUR][1000 genomes]
rs303192	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs303195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303197	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303199	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303202	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303204	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304416	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497191	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7903979	0.88[CEU][hapmap]
rs7924208	0.84[CEU][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs304430	IFIT1	cis	parietal	SCAN
rs304430	HECTD2	cis	parietal	SCAN
rs304430	NUDT9P1	cis	parietal	SCAN
rs304430	STAMBPL1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91224000-91234600	Weak transcription	Right Ventricle	heart
2	chr10:91224200-91228400	Enhancers	Fetal Heart	heart
3	chr10:91224200-91230400	Weak transcription	Left Ventricle	heart
4	chr10:91224200-91236000	Weak transcription	Lung	lung
5	chr10:91225600-91227200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:91225600-91227200	Enhancers	HMEC	breast
7	chr10:91225600-91227800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr10:91225800-91227200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:91225800-91227600	Enhancers	NHEK	skin
10	chr10:91226000-91227000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:91226000-91227000	Enhancers	HSMM	muscle
12	chr10:91226000-91227200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr10:91226000-91227200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:91226000-91227200	Enhancers	Fetal Intestine Large	intestine
15	chr10:91226000-91227400	Enhancers	A549	lung
16	chr10:91226000-91228400	Enhancers	Fetal Intestine Small	intestine
17	chr10:91226200-91227000	Enhancers	NHLF	lung
18	chr10:91226200-91227000	Enhancers	Osteobl	bone
19	chr10:91226200-91227200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:91226200-91231600	Enhancers	Fetal Lung	lung
21	chr10:91226400-91227000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:91226400-91227000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:91226400-91227000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr10:91226400-91227000	Enhancers	HUVEC	blood vessel
25	chr10:91226400-91227000	Enhancers	NH-A	brain
26	chr10:91226800-91227000	Enhancers	Rectal Smooth Muscle	rectum
27	chr10:91226800-91227200	Enhancers	Hela-S3	cervix
28	chr10:91226800-91227800	Weak transcription	Liver	Liver
29	chr10:91226800-91228000	Weak transcription	Pancreas	Pancrea
30	chr10:91226800-91228000	Weak transcription	Right Atrium	heart
31	chr10:91226800-91228000	Weak transcription	Small Intestine	intestine
32	chr10:91226800-91228200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:91226800-91229200	Weak transcription	NHDF-Ad	bronchial
34	chr10:91226800-91229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:91226800-91237800	Weak transcription	Stomach Mucosa	stomach

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