Variant report

Variant	rs1570116
Chromosome Location	chr6:36957344-36957345
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	chr6:36905749..36908241-chr6:36957017..36958838,2	K562	blood:
2	chr6:36953616..36955180-chr6:36955668..36958158,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12524747	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12524778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318960	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1318961	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13217627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16889364	0.96[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1753284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1753286	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293390	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs2770123	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35466616	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714028	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4714029	0.97[ASN][1000 genomes]
rs6915109	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6915207	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919808	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs708009	0.97[ASN][1000 genomes]
rs708011	0.96[ASN][1000 genomes]
rs708013	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7739340	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7739958	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7744277	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7762333	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs831477	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368977	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380631	0.97[ASN][1000 genomes]
rs9394393	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470451	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv602952	chr6:36951210-36978745	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1570116	PI16	cis	parietal	SCAN
rs1570116	FTSJD2	cis	brain	seeQTL
rs1570116	COG5	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36955200-36959200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:36955400-36965200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:36955400-36965400	Weak transcription	Right Atrium	heart
4	chr6:36957000-36957800	Enhancers	K562	blood

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