Variant report

Variant	rs1980277
Chromosome Location	chr3:160385339-160385340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160378138..160380305-chr3:160382789..160386961,3	K562	blood:
2	chr3:160379485..160381403-chr3:160384390..160388251,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10936203	0.80[CEU][hapmap]
rs10936207	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10936208	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10936209	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10936210	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712392	0.83[EUR][1000 genomes]
rs11713230	0.83[EUR][1000 genomes]
rs11714916	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11927913	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490985	0.82[ASN][1000 genomes]
rs12639488	0.88[CEU][hapmap]
rs13065269	0.83[EUR][1000 genomes]
rs13074231	0.83[EUR][1000 genomes]
rs13095931	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1317085	0.87[ASN][1000 genomes]
rs1403045	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236586	0.92[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1879797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882125	0.84[CEU][hapmap]
rs2141668	0.82[EUR][1000 genomes]
rs2178451	0.82[EUR][1000 genomes]
rs2178452	0.87[ASN][1000 genomes]
rs2367209	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28544045	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28730907	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34362576	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34949451	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35008770	0.82[EUR][1000 genomes]
rs35308461	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35480231	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35498840	0.84[CEU][hapmap]
rs35664264	0.87[ASN][1000 genomes]
rs35867836	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36118017	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4133253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679659	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679660	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679903	0.82[EUR][1000 genomes]
rs4679904	0.83[EUR][1000 genomes]
rs4679909	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs57718211	0.81[EUR][1000 genomes]
rs62272216	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62272217	0.87[ASN][1000 genomes]
rs62272218	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62272219	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62272220	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6763757	0.80[AMR][1000 genomes]
rs6763892	0.80[AMR][1000 genomes]
rs6773389	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774379	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6774566	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6776873	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6777739	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6779581	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6779671	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6787452	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6788429	0.80[AMR][1000 genomes]
rs6797760	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6798462	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6801373	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6803670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610939	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633839	0.84[CEU][hapmap]
rs7634255	0.84[CEU][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1980277	IFT80	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160382400-160385400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:160383400-160385600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:160383400-160386400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160383600-160385600	Enhancers	NHDF-Ad	bronchial
5	chr3:160383600-160385800	Enhancers	HMEC	breast
6	chr3:160383600-160385800	Enhancers	Osteobl	bone
7	chr3:160383600-160386200	Enhancers	Fetal Intestine Large	intestine
8	chr3:160383600-160386200	Enhancers	Fetal Intestine Small	intestine
9	chr3:160383600-160386600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:160383800-160385800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:160383800-160386400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:160384000-160385400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:160384000-160386400	Enhancers	GM12878-XiMat	blood
14	chr3:160384000-160386400	Enhancers	Hela-S3	cervix
15	chr3:160384000-160387800	Weak transcription	Small Intestine	intestine
16	chr3:160384000-160389200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:160384200-160385400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:160384200-160385800	Enhancers	NH-A	brain
19	chr3:160384800-160385600	Enhancers	NHLF	lung
20	chr3:160384800-160385800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:160384800-160385800	Enhancers	HUVEC	blood vessel
22	chr3:160384800-160385800	Enhancers	NHEK	skin
23	chr3:160384800-160386200	Enhancers	A549	lung
24	chr3:160384800-160386400	Enhancers	Stomach Mucosa	stomach
25	chr3:160385000-160385600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:160385200-160385400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:160385200-160385600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:160385200-160385600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:160385200-160385800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:160385200-160386000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:160385200-160386400	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:160385200-160395000	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links