Variant report

Variant	rs546741
Chromosome Location	chr1:72289671-72289672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11209852	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs11209853	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs11209854	0.85[CHD][hapmap]
rs12037610	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350648	0.91[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1426178	0.90[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1814054	0.82[CEU][hapmap]
rs1814055	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3909665	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs490859	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs495411	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508954	0.91[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs510012	0.83[EUR][1000 genomes]
rs517762	0.86[CHB][hapmap]
rs517901	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs545538	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs595910	0.81[EUR][1000 genomes]
rs6659202	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs6683448	0.91[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7526542	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv830181	chr1:72155983-72296578	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72287200-72292600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:72289000-72290600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:72289400-72289800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:72289400-72290000	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:72289400-72290000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:72289600-72290000	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links