Variant report

Variant	rs188589
Chromosome Location	chr10:91185592-91185593
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91184701..91187287-chr10:91403234..91405861,2	MCF-7	breast:
2	chr10:91173086..91175345-chr10:91183942..91186085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107798	Chromatin interaction
ENSG00000232936	Chromatin interaction
ENSG00000152778	Chromatin interaction
ENSG00000249962	Chromatin interaction
ENSG00000152782	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs184236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188591	0.89[EUR][1000 genomes]
rs2484046	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484047	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs303171	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303173	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303209	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs303210	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs303213	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs303215	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303216	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303218	0.97[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs304410	0.80[CEU][hapmap]
rs304411	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304412	0.81[EUR][1000 genomes]
rs304413	0.81[EUR][1000 genomes]
rs304434	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs304436	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304437	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs304441	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs304442	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs304447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304450	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs304492	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs304493	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs304497	0.80[EUR][1000 genomes]
rs304500	0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs304501	0.81[JPT][hapmap]
rs304502	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs304503	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs304505	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs304506	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs304508	0.81[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs188589	IFIT1	Cis_1M	lymphoblastoid	RTeQTL
rs188589	IFIT5	cis	Artery Tibial	GTEx
rs188589	IFIT5	cis	Esophagus Muscularis	GTEx
rs188589	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs188589	IFIT5	cis	Esophagus Mucosa	GTEx
rs188589	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91175400-91187600	Weak transcription	HUVEC	blood vessel
2	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
4	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
5	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:91178000-91186000	Weak transcription	HMEC	breast
7	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
8	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
9	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
12	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
13	chr10:91178400-91185600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr10:91178400-91186200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:91178400-91186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:91178400-91186200	Weak transcription	NHLF	lung
17	chr10:91178400-91186200	Weak transcription	Osteobl	bone
18	chr10:91178400-91187200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:91178400-91188000	Weak transcription	Right Ventricle	heart
20	chr10:91178400-91191600	Weak transcription	A549	lung
21	chr10:91178600-91186200	Weak transcription	NH-A	brain
22	chr10:91178800-91186200	Weak transcription	NHDF-Ad	bronchial
23	chr10:91178800-91186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:91179000-91186200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr10:91179400-91186400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:91179400-91187600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr10:91179400-91187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:91179400-91187800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:91179400-91187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr10:91179600-91225600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:91181200-91185600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr10:91181200-91192800	Weak transcription	Left Ventricle	heart
33	chr10:91181400-91186000	Weak transcription	Fetal Heart	heart
34	chr10:91181400-91186200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:91181400-91186200	Weak transcription	NHEK	skin
36	chr10:91181600-91186200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:91181600-91186200	Weak transcription	HSMM	muscle
38	chr10:91181800-91186200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:91181800-91186400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:91182000-91185600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr10:91182000-91186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:91182000-91186400	Weak transcription	Fetal Lung	lung
43	chr10:91182000-91187200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr10:91182200-91187400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:91182200-91191200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:91182200-91191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:91183800-91186400	Enhancers	HepG2	liver
48	chr10:91184400-91186200	Enhancers	Liver	Liver
49	chr10:91184600-91186000	Weak transcription	Fetal Kidney	kidney
50	chr10:91184600-91186200	Enhancers	Fetal Intestine Large	intestine

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