Variant report

Variant	rs202906
Chromosome Location	chr6:28011652-28011653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28011563-28011776	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28004584..28007238-chr6:28010224..28013138,2	K562	blood:
2	chr6:27861805..27863822-chr6:28010938..28012589,2	MCF-7	breast:
3	chr6:27797828..27799356-chr6:28009972..28012647,2	K562	blood:
4	chr6:28008244..28009749-chr6:28011641..28013622,2	K562	blood:
5	chr6:28010916..28013781-chr6:28060247..28062544,2	K562	blood:
6	chr6:28004519..28007774-chr6:28009594..28013138,4	K562	blood:
7	chr6:28011209..28013344-chr6:28013937..28015849,2	K562	blood:

No data

Variant related genes	Relation type
OR2B7P	TF binding region
ENSG00000187763	Chromatin interaction
ENSG00000197914	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1015075	0.95[CHD][hapmap];1.00[GIH][hapmap]
rs12055625	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs13194781	0.80[CEU][hapmap]
rs13195291	0.80[CEU][hapmap]
rs13197633	0.80[CEU][hapmap]
rs13199649	0.80[CEU][hapmap]
rs13199772	0.80[CEU][hapmap]
rs13199906	0.80[CEU][hapmap]
rs13200214	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs13201308	0.80[CEU][hapmap]
rs13205211	0.80[CEU][hapmap]
rs1321504	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1321505	1.00[CHB][hapmap]
rs13218875	0.80[CEU][hapmap]
rs149943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs149949	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs156743	0.94[EUR][1000 genomes]
rs16893573	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16893601	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs16893735	1.00[CHB][hapmap]
rs17695758	0.80[CEU][hapmap]
rs17763089	0.80[CEU][hapmap]
rs188015	0.86[EUR][1000 genomes]
rs200948	0.90[CEU][hapmap]
rs200949	0.90[CEU][hapmap]
rs200953	0.90[CEU][hapmap]
rs200954	0.90[CEU][hapmap]
rs200977	0.90[CEU][hapmap]
rs200981	0.90[CEU][hapmap]
rs200989	0.90[CEU][hapmap]
rs200990	0.90[CEU][hapmap]
rs200995	0.90[CEU][hapmap]
rs3734571	1.00[CHB][hapmap]
rs3757188	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs4713138	1.00[CHB][hapmap]
rs4713139	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs4713140	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs735765	0.85[CHD][hapmap]
rs904142	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9348789	0.90[JPT][hapmap]
rs9380028	0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9380030	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9380031	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9380032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9380041	0.81[ASN][1000 genomes]
rs9380045	0.84[JPT][hapmap]
rs9380051	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9380064	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9393882	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9393902	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9468271	0.84[JPT][hapmap]
rs9468275	0.91[JPT][hapmap]
rs9468287	1.00[CHB][hapmap];0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs202906	HIST1H4F	cis	parietal	SCAN
rs202906	LRRC16A	cis	parietal	SCAN
rs202906	ZNF192	cis	cerebellum	SCAN
rs202906	SLC17A2	cis	cerebellum	SCAN
rs202906	CMAH	cis	parietal	SCAN
rs202906	BTN3A2	cis	multi-tissue	Pritchard
rs202906	HIST1H2BC	cis	parietal	SCAN
rs202906	HLA-H	cis	multi-tissue	Pritchard
rs202906	ZSCAN23	cis	cerebellum	SCAN
rs202906	AL022393.7	cis	Muscle Skeletal	GTEx
rs202906	ZNF323	cis	parietal	SCAN
rs202906	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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