Variant report

Variant	rs11098275
Chromosome Location	chr4:79536646-79536647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79536352..79538431-chr4:79574021..79576567,2	K562	blood:
2	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
3	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
4	chr4:79534658..79536722-chr4:79591597..79593371,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10008069	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs10028815	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10029214	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10857035	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098274	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098278	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11725235	0.81[JPT][hapmap]
rs11932080	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12510383	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644222	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12711028	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13110339	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1346145	0.81[TSI][hapmap]
rs1532427	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806906	0.88[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1834519	0.84[TSI][hapmap]
rs28579596	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34636970	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254805	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4365753	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4472163	0.81[TSI][hapmap]
rs4495064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4560439	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4645238	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5942	0.81[JPT][hapmap]
rs5944	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308286	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6533827	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6533828	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6815367	0.80[AMR][1000 genomes]
rs6817175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6821449	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822675	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825328	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855458	0.84[TSI][hapmap]
rs7656801	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7659978	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661370	0.81[JPT][hapmap]
rs7672835	0.87[CEU][hapmap]
rs7672903	0.85[JPT][hapmap]
rs7675464	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7675646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677783	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7694152	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11098275	CXCL10	cis	parietal	SCAN
rs11098275	LOC643424	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491800-79542600	Weak transcription	NH-A	brain
2	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
5	chr4:79524200-79543400	Weak transcription	A549	lung
6	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:79529400-79537600	Enhancers	Dnd41	blood
9	chr4:79529800-79537000	Enhancers	Primary hematopoietic stem cells	blood
10	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
11	chr4:79531200-79536800	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
13	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
14	chr4:79532000-79536800	Enhancers	Fetal Thymus	thymus
15	chr4:79532000-79537200	Weak transcription	HSMM	muscle
16	chr4:79532400-79536800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:79532400-79537200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:79532400-79537200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:79532600-79537200	Weak transcription	NHDF-Ad	bronchial
20	chr4:79533200-79536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:79533800-79538600	Enhancers	Fetal Intestine Large	intestine
22	chr4:79533800-79541000	Enhancers	Fetal Intestine Small	intestine
23	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:79534200-79537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:79534200-79537200	Weak transcription	HMEC	breast
26	chr4:79534200-79537200	Weak transcription	NHEK	skin
27	chr4:79534600-79536800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:79534600-79547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:79534800-79537000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:79534800-79538200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:79535200-79538000	Enhancers	K562	blood
32	chr4:79535400-79542600	Weak transcription	Placenta	Placenta
33	chr4:79535600-79539200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:79535600-79543000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:79535800-79536800	Enhancers	GM12878-XiMat	blood
36	chr4:79536000-79536800	Enhancers	Fetal Heart	heart
37	chr4:79536200-79536800	Enhancers	Right Atrium	heart
38	chr4:79536200-79537000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:79536200-79538200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr4:79536200-79538600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:79536200-79538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:79536400-79538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
44	chr4:79536600-79536800	Enhancers	Thymus	Thymus
45	chr4:79536600-79538600	Weak transcription	Primary B cells from cord blood	blood

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