Variant report

Variant	rs12617866
Chromosome Location	chr2:234838741-234838742
allele	C/T
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:30)

rs_ID	r²[population]
rs11562956	0.85[YRI][hapmap]
rs11562977	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs11563214	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11563218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12620352	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468521	1.00[EUR][1000 genomes]
rs16849914	0.83[YRI][hapmap]
rs2362291	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28900710	0.85[YRI][hapmap]
rs28900713	0.85[YRI][hapmap]
rs28901579	1.00[EUR][1000 genomes]
rs28901582	1.00[EUR][1000 genomes]
rs28901591	0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs28901600	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28901608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901615	1.00[EUR][1000 genomes]
rs28901618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901629	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901630	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs28901637	1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28901868	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs28902174	0.83[EUR][1000 genomes]
rs4663342	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663343	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4663989	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602303	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9789366	0.93[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9789398	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs9789675	0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234837400-234839000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr2:234837600-234838800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr2:234837600-234838800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr2:234837600-234839000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:234837600-234839000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:234837800-234838800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:234837800-234839000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr2:234838000-234838800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:234838000-234838800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:234838000-234838800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:234838000-234838800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:234838400-234839400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:234838400-234839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:234838400-234841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:234838600-234841000	Weak transcription	H9 Cell Line	embryonic stem cell

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