Variant report

Variant	rs12477261
Chromosome Location	chr2:151616147-151616148
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10191762	0.98[EUR][1000 genomes]
rs1028216	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1028217	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1028218	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10803820	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13000349	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401802	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401804	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1519790	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1519791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2013081	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727272	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568086	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs925986	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs969912	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2756950	chr2:151502539-151749973	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv834416	chr2:151517784-151699912	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010993	chr2:151535786-151742522	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv35134	chr2:151542492-151741492	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477261	RIF1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151612600-151616600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:151614000-151616200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:151614000-151618800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:151615600-151616400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:151615800-151616400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:151615800-151616400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:151615800-151616400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:151615800-151616600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:151616000-151616400	Enhancers	Fetal Lung	lung
10	chr2:151616000-151616600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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