Variant report

Variant	rs3731659
Chromosome Location	chr2:98921826-98921827
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	chr2:98903777..98907619-chr2:98918307..98922639,4	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10172281	0.81[ASN][1000 genomes]
rs10176056	0.98[ASN][1000 genomes]
rs10181000	0.87[CHB][hapmap]
rs10190336	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs10201994	0.98[ASN][1000 genomes]
rs10202618	0.96[ASN][1000 genomes]
rs10203437	0.96[ASN][1000 genomes]
rs11124096	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs11124107	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124121	0.85[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11679920	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11889349	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs11891512	0.80[ASN][1000 genomes]
rs11895654	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs11901562	0.90[ASN][1000 genomes]
rs12478763	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12478769	0.80[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12624294	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712256	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12993718	0.80[ASN][1000 genomes]
rs12999985	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13013876	0.80[ASN][1000 genomes]
rs13014142	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13033263	0.80[ASN][1000 genomes]
rs13394706	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13408372	0.85[CHB][hapmap]
rs13415414	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13428221	0.85[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1504679	0.96[ASN][1000 genomes]
rs17427684	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17428056	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap]
rs17493655	0.98[ASN][1000 genomes]
rs17493788	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1875880	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2102270	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs2122756	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2202387	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2221416	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4374424	1.00[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4389366	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap]
rs4477970	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.80[ASN][1000 genomes]
rs4479470	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4494805	0.80[ASN][1000 genomes]
rs4608580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632400	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4851122	0.90[ASN][1000 genomes]
rs4851123	0.96[ASN][1000 genomes]
rs4851124	1.00[ASN][1000 genomes]
rs4851935	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4851951	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.80[ASN][1000 genomes]
rs4851954	0.92[ASN][1000 genomes]
rs4851955	0.96[ASN][1000 genomes]
rs4851959	1.00[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs56320609	0.81[ASN][1000 genomes]
rs62157914	0.98[ASN][1000 genomes]
rs6543419	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs6543459	0.98[ASN][1000 genomes]
rs66464436	0.98[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs6725543	0.91[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742930	1.00[ASN][1000 genomes]
rs6747344	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6747410	0.87[CHB][hapmap]
rs6750975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap]
rs72819909	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72933220	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572757	0.98[ASN][1000 genomes]
rs7574218	0.80[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs7589018	0.98[ASN][1000 genomes]
rs7598554	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7606070	0.96[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap]
rs937726	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3731659	ANKRD39	cis	parietal	SCAN
rs3731659	TMEM127	cis	parietal	SCAN
rs3731659	FAM38B	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98917000-98926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:98917200-98924400	Weak transcription	Gastric	stomach
3	chr2:98918800-98928600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:98921800-98926000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links