Variant report

Variant	rs2367209
Chromosome Location	chr3:160398885-160398886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160396356..160398268-chr3:160398713..160401566,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10460866	0.84[EUR][1000 genomes]
rs10936210	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11709300	0.81[ASN][1000 genomes]
rs11714916	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720693	0.88[EUR][1000 genomes]
rs11927913	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13062928	0.86[EUR][1000 genomes]
rs13065289	0.82[ASN][1000 genomes]
rs13072556	0.85[EUR][1000 genomes]
rs13075424	0.81[EUR][1000 genomes]
rs13085507	0.86[EUR][1000 genomes]
rs1403045	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1522285	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16831337	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17236586	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1879797	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1882125	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1980277	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34058107	0.88[EUR][1000 genomes]
rs34444753	0.93[EUR][1000 genomes]
rs35498840	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4133253	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4679909	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4679910	0.82[ASN][1000 genomes]
rs57718211	0.90[EUR][1000 genomes]
rs60339919	0.93[EUR][1000 genomes]
rs62272215	0.82[ASN][1000 genomes]
rs62272220	0.81[ASN][1000 genomes]
rs6763757	0.83[ASN][1000 genomes]
rs6763892	0.83[ASN][1000 genomes]
rs6773962	0.82[ASN][1000 genomes]
rs6777739	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6779581	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs6779671	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs6788429	0.83[ASN][1000 genomes]
rs6788886	0.82[ASN][1000 genomes]
rs6792943	0.93[EUR][1000 genomes]
rs6798462	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6801636	0.82[ASN][1000 genomes]
rs6803670	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6806755	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71314011	0.84[EUR][1000 genomes]
rs7610939	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.87[MKK][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7632884	0.82[ASN][1000 genomes]
rs7633839	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7634255	0.92[CEU][hapmap];0.84[MEX][hapmap];0.82[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2367209	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs2367209	IFT80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160395600-160401600	Weak transcription	Gastric	stomach
2	chr3:160395600-160401800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:160395800-160400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:160397000-160412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:160397200-160401800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:160397400-160399000	Enhancers	Fetal Intestine Small	intestine
7	chr3:160397400-160400800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:160397400-160401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:160397400-160401600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:160397400-160401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:160397400-160403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:160397600-160401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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