Variant report

Variant	rs2465854
Chromosome Location	chr6:161310910-161310911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1247298	0.81[JPT][hapmap]
rs1247299	0.81[JPT][hapmap]
rs1247308	0.81[JPT][hapmap]
rs1247309	0.81[JPT][hapmap]
rs1247313	0.81[JPT][hapmap]
rs1247322	0.81[JPT][hapmap]
rs1247323	0.81[JPT][hapmap]
rs1247325	0.81[JPT][hapmap]
rs1247327	0.81[JPT][hapmap]
rs1247360	0.81[JPT][hapmap]
rs1247361	0.81[JPT][hapmap]
rs1247363	0.81[JPT][hapmap]
rs1247537	0.92[CHB][hapmap]
rs1317216	0.82[EUR][1000 genomes]
rs1937480	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1937483	0.95[ASN][1000 genomes]
rs2465834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465841	0.95[ASN][1000 genomes]
rs2465842	0.92[ASN][1000 genomes]
rs2465843	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465844	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465872	0.97[ASN][1000 genomes]
rs2465873	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465874	0.97[ASN][1000 genomes]
rs2465875	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465876	0.87[JPT][hapmap]
rs2465877	0.87[JPT][hapmap]
rs2489935	0.82[EUR][1000 genomes]
rs2489939	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2489944	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2489945	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2489946	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489947	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489955	0.87[JPT][hapmap]
rs2489956	0.87[JPT][hapmap]
rs57196352	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57300662	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765351	0.81[CHB][hapmap]
rs9347466	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9364580	0.87[JPT][hapmap]
rs9365229	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[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	esv3352911	chr6:161140543-161324358	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1837673	chr6:161216608-161318009	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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
rs2465854	SLC22A2	cis	parietal	SCAN
rs2465854	SNORA29	cis	parietal	SCAN
rs2465854	SLC22A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161296000-161313000	Weak transcription	Right Atrium	heart
2	chr6:161302800-161316600	Weak transcription	Ovary	ovary
3	chr6:161305400-161312200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:161307200-161311400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:161309800-161311000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:161310000-161311000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:161310200-161311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:161310600-161311400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:161310600-161311600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:161310800-161311000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr6:161310800-161315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:161310800-161316400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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