Variant report

Variant	rs2465834
Chromosome Location	chr6:161301868-161301869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161300742..161302528-chr6:161411919..161413550,2	K562	blood:

Variant related genes	Relation type
ENSG00000272841	Chromatin interaction
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

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	0.90[CHB][hapmap]
rs1317216	0.82[EUR][1000 genomes]
rs1937480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1937483	0.93[ASN][1000 genomes]
rs2465841	0.93[ASN][1000 genomes]
rs2465842	0.90[ASN][1000 genomes]
rs2465843	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465854	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465872	0.96[ASN][1000 genomes]
rs2465873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465874	0.96[ASN][1000 genomes]
rs2465875	0.80[EUR][1000 genomes];0.93[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]
rs2489944	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489945	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2489946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2489947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2489955	0.87[JPT][hapmap]
rs2489956	0.87[JPT][hapmap]
rs57196352	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57300662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9347466	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9364580	0.87[JPT][hapmap]
rs9365229	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];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	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
rs2465834	SLC22A2	cis	cerebellum	SCAN
rs2465834	SLC22A2	cis	parietal	SCAN
rs2465834	SNORA29	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161294200-161304200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:161296000-161313000	Weak transcription	Right Atrium	heart
3	chr6:161298000-161303800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:161298200-161305200	Weak transcription	Pancreas	Pancrea
5	chr6:161298800-161302400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:161298800-161305000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:161299200-161304200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:161299400-161302400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:161299600-161302000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:161299600-161302200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:161299800-161302000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:161300000-161302000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:161301400-161303800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:161301600-161302000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:161301600-161302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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