Variant report

Variant	rs1587222
Chromosome Location	chr4:79515724-79515725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79514162..79516035-chr4:79524140..79525956,2	K562	blood:
2	chr4:79515008..79517115-chr4:79611076..79613175,2	K562	blood:
3	chr4:79513931..79517540-chr4:79518981..79521384,5	K562	blood:
4	chr4:79513623..79515338-chr4:79515610..79517410,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10001246	0.85[JPT][hapmap]
rs10003947	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11098257	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11733269	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs12641838	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs12642521	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs13126934	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1472365	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs1874486	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1874487	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs2867462	0.87[ASN][1000 genomes]
rs3805174	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs3805175	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4466067	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs4975147	1.00[CHB][hapmap]
rs6533804	0.87[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs6533821	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs6851992	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7654600	1.00[CHB][hapmap]
rs7656476	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs7679218	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7683399	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7683582	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs867677	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9307409	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs950699	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1587222	ANXA3	cis	cerebellum	SCAN
rs1587222	LOC643424	cis	multi-tissue	Pritchard
rs1587222	CXCL10	cis	parietal	SCAN

Chromatin state (count:55 , 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	chr4:79490000-79523400	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:79490600-79521000	Weak transcription	Fetal Heart	heart
8	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
10	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:79491800-79542600	Weak transcription	NH-A	brain
13	chr4:79492000-79531600	Strong transcription	HMEC	breast
14	chr4:79500000-79522200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:79501400-79516000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
17	chr4:79502400-79525800	Weak transcription	Psoas Muscle	Psoas
18	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:79503200-79521800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:79505800-79517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:79506400-79517200	Weak transcription	Pancreas	Pancrea
22	chr4:79506400-79517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:79506800-79523800	Weak transcription	Placenta	Placenta
24	chr4:79507600-79521000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:79508600-79523600	Weak transcription	Adipose Nuclei	Adipose
27	chr4:79508800-79525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:79508800-79527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:79508800-79527400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:79510000-79517200	Weak transcription	Fetal Stomach	stomach
31	chr4:79510000-79518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:79510000-79520600	Weak transcription	Lung	lung
33	chr4:79510800-79520800	Weak transcription	Left Ventricle	heart
34	chr4:79510800-79523400	Weak transcription	A549	lung
35	chr4:79511000-79523800	Weak transcription	Hela-S3	cervix
36	chr4:79512400-79523600	Weak transcription	Gastric	stomach
37	chr4:79512400-79524400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:79512800-79525600	Weak transcription	NHLF	lung
41	chr4:79513600-79516400	Strong transcription	Fetal Intestine Large	intestine
42	chr4:79513600-79516400	Weak transcription	HUVEC	blood vessel
43	chr4:79513600-79516600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:79513600-79517200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:79513600-79521000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr4:79513800-79516800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:79513800-79521000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:79513800-79534200	Strong transcription	NHEK	skin
49	chr4:79514000-79516000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:79514000-79517000	Weak transcription	Stomach Mucosa	stomach

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