Variant report

Variant	rs304411
Chromosome Location	chr10:91186881-91186882
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:91184701..91187287-chr10:91403234..91405861,2	MCF-7	breast:
2	chr10:91186724..91190191-chr10:91191424..91194193,3	K562	blood:
3	chr10:91009894..91012691-chr10:91185718..91187496,2	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10788641	0.85[MEX][hapmap]
rs10887946	1.00[MEX][hapmap]
rs11203078	1.00[MEX][hapmap]
rs184236	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs188589	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]
rs188591	0.87[EUR][1000 genomes]
rs2484046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2484047	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs303168	1.00[YRI][hapmap]
rs303171	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs303173	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303208	0.85[MEX][hapmap]
rs303209	0.84[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303210	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303213	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303215	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs303216	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs303218	0.82[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304410	0.83[JPT][hapmap]
rs304412	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs304413	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs304434	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs304436	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs304437	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304441	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs304442	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs304447	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs304492	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304498	0.82[CEU][hapmap]
rs304500	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs304501	0.85[MEX][hapmap]
rs304502	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs304503	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304505	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304506	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304508	0.84[MEX][hapmap]
rs627127	0.80[MEX][hapmap]
rs6586209	1.00[YRI][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs304411	IDE	cis	parietal	SCAN
rs304411	IFIT5	cis	parietal	SCAN
rs304411	IFIT1	Cis_1M	lymphoblastoid	RTeQTL
rs304411	IFIT5	cis	Nerve Tibial	GTEx
rs304411	IFIT5	cis	Esophagus Muscularis	GTEx
rs304411	IFIT5	cis	Thyroid	GTEx
rs304411	IFIT5	cis	cerebellum	SCAN
rs304411	IFIT5	cis	Artery Tibial	GTEx
rs304411	LIPA	cis	parietal	SCAN
rs304411	IFIT1	cis	cerebellum	SCAN
rs304411	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304411	IFIT5	cis	lymphoblastoid	seeQTL
rs304411	IFIT5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:45 , 50 per page) page: 1

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	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
7	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
8	chr10:91178400-91187200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:91178400-91188000	Weak transcription	Right Ventricle	heart
10	chr10:91178400-91191600	Weak transcription	A549	lung
11	chr10:91179400-91187600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:91179400-91187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:91179400-91187800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:91179400-91187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:91179600-91225600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:91181200-91192800	Weak transcription	Left Ventricle	heart
17	chr10:91182000-91187200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr10:91182200-91187400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:91182200-91191200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr10:91182200-91191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:91186000-91189000	Enhancers	HMEC	breast
22	chr10:91186000-91189600	Enhancers	Fetal Heart	heart
23	chr10:91186200-91187000	Enhancers	HSMMtube	muscle
24	chr10:91186200-91187200	Enhancers	NH-A	brain
25	chr10:91186200-91187800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr10:91186200-91188400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:91186200-91188400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:91186200-91188400	Enhancers	NHLF	lung
29	chr10:91186200-91188400	Enhancers	Osteobl	bone
30	chr10:91186200-91188800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:91186200-91189000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:91186200-91189000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:91186200-91189000	Enhancers	NHEK	skin
34	chr10:91186200-91189400	Enhancers	HSMM	muscle
35	chr10:91186200-91189800	Enhancers	NHDF-Ad	bronchial
36	chr10:91186400-91187800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr10:91186400-91188600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr10:91186400-91188800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:91186400-91189000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:91186400-91189000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:91186400-91189000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:91186600-91187800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:91186600-91187800	Weak transcription	Right Atrium	heart
44	chr10:91186600-91188000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr10:91186600-91188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links