Variant report

Variant	rs2867461
Chromosome Location	chr4:79513215-79513216
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	chr4:79509559..79512008-chr4:79512168..79514182,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10028001	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642521	0.80[MEX][hapmap]
rs13127051	0.85[ASN][1000 genomes]
rs1546177	0.82[CHB][hapmap]
rs1874486	0.80[MEX][hapmap]
rs3805174	0.80[MEX][hapmap]
rs4975071	0.86[CHB][hapmap]
rs7656476	0.80[MEX][hapmap]
rs7672835	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7683399	0.80[MEX][hapmap]
rs868079	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv967949	chr4:79511515-79527707	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	22446963	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2867461	CXCL10	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
2	chr4:79481800-79521000	Weak transcription	Right Ventricle	heart
3	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:79488400-79523600	Weak transcription	Esophagus	oesophagus
5	chr4:79488400-79527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:79489800-79513600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:79490000-79523400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:79490600-79521000	Weak transcription	Fetal Heart	heart
9	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
11	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:79491800-79542600	Weak transcription	NH-A	brain
14	chr4:79492000-79531600	Strong transcription	HMEC	breast
15	chr4:79500000-79522200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:79501400-79516000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
18	chr4:79502400-79525800	Weak transcription	Psoas Muscle	Psoas
19	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:79503200-79521800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:79505800-79517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:79506400-79517200	Weak transcription	Pancreas	Pancrea
23	chr4:79506400-79517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:79506800-79523800	Weak transcription	Placenta	Placenta
25	chr4:79507000-79513400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:79507000-79513400	Weak transcription	K562	blood
27	chr4:79507600-79521000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:79508600-79523600	Weak transcription	Adipose Nuclei	Adipose
30	chr4:79508800-79525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:79508800-79527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:79508800-79527400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:79509600-79515200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:79510000-79517200	Weak transcription	Fetal Stomach	stomach
35	chr4:79510000-79518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:79510000-79520600	Weak transcription	Lung	lung
37	chr4:79510400-79513600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:79510600-79513600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:79510800-79513400	Weak transcription	Right Atrium	heart
40	chr4:79510800-79514200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:79510800-79520800	Weak transcription	Left Ventricle	heart
42	chr4:79510800-79523400	Weak transcription	A549	lung
43	chr4:79511000-79523800	Weak transcription	Hela-S3	cervix
44	chr4:79511200-79513400	Weak transcription	Fetal Intestine Large	intestine
45	chr4:79512000-79513600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:79512000-79513800	Genic enhancers	NHEK	skin
47	chr4:79512200-79513600	Enhancers	HUVEC	blood vessel
48	chr4:79512400-79513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:79512400-79513400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:79512400-79513400	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links