Variant report

Variant	rs7775820
Chromosome Location	chr6:25734800-25734801
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	chr6:25726874..25732773-chr6:25733816..25737170,6	K562	blood:

Variant related genes	Relation type
ENSG00000216436	Chromatin interaction
ENSG00000178762	Chromatin interaction
ENSG00000146047	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10105	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10484431	1.00[JPT][hapmap]
rs11751287	0.85[EUR][1000 genomes]
rs11751622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964886	1.00[JPT][hapmap]
rs11969868	1.00[JPT][hapmap]
rs16890970	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16891142	1.00[JPT][hapmap]
rs17320614	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275906	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs28360622	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28385589	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34438249	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34582964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34589724	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3734524	1.00[JPT][hapmap]
rs4236039	0.88[CEU][hapmap];0.92[CHD][hapmap]
rs4343909	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4351252	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911522	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs6935084	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746944	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771468	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776065	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461196	0.84[EUR][1000 genomes]
rs9461199	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9461201	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9467576	0.85[EUR][1000 genomes]
rs9467577	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9467578	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9467583	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467590	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885831	0.87[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9986459	0.87[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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv969355	chr6:25733459-25779530	Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7775820	BTN3A2	cis	cerebellum	SCAN
rs7775820	HIST1H4L	cis	cerebellum	SCAN
rs7775820	ZSCAN23	cis	cerebellum	SCAN
rs7775820	ZNF192	cis	cerebellum	SCAN
rs7775820	HIST1H4F	cis	cerebellum	SCAN
rs7775820	NKAPL	cis	cerebellum	SCAN
rs7775820	ZSCAN23	cis	parietal	SCAN
rs7775820	BTN3A2	cis	parietal	SCAN
rs7775820	HIST1H2AH	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25734800-25735400	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links