Variant report

Variant	rs12477604
Chromosome Location	chr2:187987389-187987390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALCRL-3	chr2:187987289-187987588	NONHSAT076009

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10205822	0.86[CEU][hapmap]
rs10931272	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11894779	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11902984	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12465733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs12471570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12614343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12616398	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13000137	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13005588	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16828625	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2370735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs34460383	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34938912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs35252928	0.83[AMR][1000 genomes]
rs35995403	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667138	0.86[CEU][hapmap]
rs56121767	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6733991	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72904956	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72910639	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[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	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv875553	chr2:187856937-188067355	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834486	chr2:187876328-188032965	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv431857	chr2:187930023-188098798	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1003061	chr2:187950057-188282330	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1000617	chr2:187950057-188290511	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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