Variant report

Variant	rs4495064
Chromosome Location	chr4:79550409-79550410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79542556..79545467-chr4:79549942..79551796,4	K562	blood:
2	chr4:79549970..79552473-chr4:79560389..79564299,4	K562	blood:
3	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
4	chr4:79549841..79552363-chr4:79696027..79698127,2	MCF-7	breast:
5	chr4:79547404..79551814-chr4:79694410..79698430,6	K562	blood:
6	chr4:79548752..79551333-chr4:79698595..79700948,2	K562	blood:
7	chr4:79550103..79553175-chr4:79717288..79720915,3	K562	blood:
8	chr4:79549039..79550674-chr4:79611784..79614679,2	K562	blood:
9	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
10	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
11	chr4:79547404..79553256-chr4:79694666..79698430,7	K562	blood:
12	chr4:79527750..79532040-chr4:79547937..79551505,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000238816	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10008069	0.91[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs10028457	0.93[YRI][hapmap]
rs10028815	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10029214	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]
rs10857035	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098274	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11098275	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11098278	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932080	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11944942	0.89[YRI][hapmap]
rs12510383	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12510411	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12639656	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12644222	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12711028	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13110339	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1346145	0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1532427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1806906	0.87[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs1834519	0.87[TSI][hapmap]
rs28579596	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34636970	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4074675	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4254805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257676	0.85[JPT][hapmap]
rs4264856	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs4365753	0.80[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs4472163	0.84[TSI][hapmap]
rs4560439	0.80[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs4612	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4619914	0.85[JPT][hapmap]
rs4645238	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5944	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62308286	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533828	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815367	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6817175	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6821449	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6822675	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6825328	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6842686	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6842723	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6855458	0.87[TSI][hapmap]
rs7656801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7659978	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662620	0.88[LWK][hapmap];0.94[YRI][hapmap]
rs7672835	0.86[CEU][hapmap]
rs7675464	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7675646	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7677783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699905	0.82[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4495064	ANXA3	cis	cerebellum	SCAN
rs4495064	CXCL10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
2	chr4:79542200-79555600	Enhancers	Fetal Intestine Small	intestine
3	chr4:79542600-79555600	Enhancers	Fetal Intestine Large	intestine
4	chr4:79544200-79550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:79545800-79550800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:79546600-79553000	Enhancers	Placenta	Placenta
7	chr4:79547600-79551800	Enhancers	Stomach Mucosa	stomach
8	chr4:79548000-79551800	Enhancers	HepG2	liver
9	chr4:79548000-79553200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr4:79548200-79551200	Weak transcription	Colonic Mucosa	Colon
11	chr4:79548200-79552600	Enhancers	Duodenum Mucosa	Duodenum
12	chr4:79548200-79555000	Weak transcription	Osteobl	bone
13	chr4:79548600-79553600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:79548800-79552200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr4:79548800-79557400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:79549000-79550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:79549000-79550600	Weak transcription	Brain Substantia Nigra	brain
18	chr4:79549600-79550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:79549600-79551800	Weak transcription	Small Intestine	intestine
20	chr4:79549600-79560000	Weak transcription	HMEC	breast
21	chr4:79549800-79551600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
22	chr4:79549800-79551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:79549800-79551600	Enhancers	Fetal Kidney	kidney
24	chr4:79549800-79552000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:79549800-79552000	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr4:79549800-79554200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:79550000-79551400	Enhancers	Primary B cells from cord blood	blood
28	chr4:79550000-79551600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:79550000-79552000	Enhancers	Hela-S3	cervix
30	chr4:79550000-79552200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr4:79550000-79552800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr4:79550200-79550600	Flanking Active TSS	GM12878-XiMat	blood
33	chr4:79550200-79550600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:79550200-79550800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:79550200-79550800	Enhancers	Gastric	stomach
36	chr4:79550200-79551200	Weak transcription	Brain Angular Gyrus	brain
37	chr4:79550200-79551200	Weak transcription	Right Atrium	heart
38	chr4:79550200-79551200	Enhancers	Dnd41	blood
39	chr4:79550200-79551400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr4:79550200-79551400	Enhancers	Pancreas	Pancrea
41	chr4:79550200-79551400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr4:79550200-79551600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:79550200-79552000	Enhancers	Brain Anterior Caudate	brain
44	chr4:79550200-79552200	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:79550200-79553200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr4:79550200-79556600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:79550400-79550600	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr4:79550400-79550800	Active TSS	K562	blood
49	chr4:79550400-79551000	Enhancers	Fetal Brain Male	brain
50	chr4:79550400-79551200	Enhancers	Brain Hippocampus Middle	brain

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