Variant report

Variant	rs10029214
Chromosome Location	chr4:79529206-79529207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79527063..79529896-chr4:79532184..79534959,3	K562	blood:
2	chr4:79527982..79531762-chr4:79696305..79699139,4	MCF-7	breast:
3	chr4:79527192..79529448-chr4:79696631..79698650,2	K562	blood:
4	chr4:79527750..79532040-chr4:79547937..79551505,3	K562	blood:
5	chr4:79529076..79531360-chr4:79643005..79644726,2	K562	blood:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10008069	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs10028457	0.93[YRI][hapmap]
rs10028815	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857035	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11098274	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098275	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098278	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11932080	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11944942	0.89[YRI][hapmap]
rs12510383	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510411	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12639656	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12644222	0.84[EUR][1000 genomes]
rs12711028	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13110339	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1346145	0.81[TSI][hapmap]
rs1532427	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1806906	0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs1834519	0.84[TSI][hapmap]
rs28579596	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34636970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4254805	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4365753	0.84[TSI][hapmap]
rs4472163	0.81[TSI][hapmap]
rs4495064	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4560439	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4612	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4645238	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5944	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62308286	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6533827	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6533828	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6815367	0.81[AMR][1000 genomes]
rs6817175	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6821449	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6822675	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6825328	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6842686	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6842723	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6855458	0.84[TSI][hapmap]
rs7656801	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7659978	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7662620	0.94[YRI][hapmap]
rs7672835	0.87[CEU][hapmap]
rs7675464	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7675646	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7677783	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10029214	CXCL10	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
4	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:79491800-79542600	Weak transcription	NH-A	brain
7	chr4:79492000-79531600	Strong transcription	HMEC	breast
8	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:79513800-79534200	Strong transcription	NHEK	skin
13	chr4:79517200-79534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
16	chr4:79521400-79529800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:79521400-79534000	Weak transcription	Right Ventricle	heart
18	chr4:79522200-79529600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:79522600-79531200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:79522600-79531600	Weak transcription	HSMMtube	muscle
21	chr4:79523600-79533800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:79524200-79529800	Weak transcription	Fetal Heart	heart
23	chr4:79524200-79543400	Weak transcription	A549	lung
24	chr4:79524400-79530400	Weak transcription	Hela-S3	cervix
25	chr4:79524400-79532000	Weak transcription	Pancreas	Pancrea
26	chr4:79524400-79534000	Weak transcription	Placenta	Placenta
27	chr4:79524800-79530000	Weak transcription	Primary T cells from cord blood	blood
28	chr4:79525000-79529600	Weak transcription	K562	blood
29	chr4:79525000-79529800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:79525600-79531600	Weak transcription	Thymus	Thymus
31	chr4:79527600-79529400	Weak transcription	Esophagus	oesophagus
32	chr4:79527800-79529400	Weak transcription	Adipose Nuclei	Adipose
33	chr4:79527800-79530000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:79527800-79533200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:79527800-79533800	Weak transcription	Fetal Stomach	stomach
36	chr4:79527800-79534000	Weak transcription	Spleen	Spleen
37	chr4:79527800-79534800	Weak transcription	Gastric	stomach
38	chr4:79527800-79535200	Weak transcription	Left Ventricle	heart
39	chr4:79527800-79535200	Weak transcription	Lung	lung
40	chr4:79527800-79535400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:79528000-79530000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr4:79528000-79534800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:79528200-79531200	Weak transcription	Fetal Intestine Large	intestine
46	chr4:79528200-79531200	Weak transcription	HUVEC	blood vessel
47	chr4:79528400-79534800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:79528600-79532000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:79528800-79531600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:79528800-79534000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links