Variant report

Variant	rs2460646
Chromosome Location	chr15:56642876-56642877
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11630363	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs11633374	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855094	0.95[CHB][hapmap]
rs12900678	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905899	1.00[CEU][hapmap]
rs12908734	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12911427	0.96[CEU][hapmap]
rs1402177	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477590	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1549452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554410	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16976890	0.95[CHB][hapmap]
rs17819438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2114183	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2303441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2465973	0.84[EUR][1000 genomes]
rs2554287	0.95[CHB][hapmap]
rs2682012	0.83[ASN][1000 genomes]
rs2682019	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682021	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682023	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2682053	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2682054	1.00[CEU][hapmap]
rs2682059	0.96[CEU][hapmap]
rs2713924	1.00[CEU][hapmap]
rs2713933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2713935	0.82[CEU][hapmap]
rs2713936	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2713941	1.00[CEU][hapmap]
rs2718901	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2718921	0.95[CHB][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap]
rs2725854	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2725856	0.86[CHB][hapmap]
rs2725862	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34755898	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35497167	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35863560	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784552	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817406	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3985758	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774859	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62022122	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022127	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022133	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493856	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493858	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7170307	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7174892	0.88[ASN][1000 genomes]
rs7181235	0.95[CHB][hapmap]
rs7181320	0.89[CEU][hapmap]
rs7496402	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs795786	0.82[CHB][hapmap]
rs795791	0.91[CHB][hapmap]
rs795800	0.95[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2460646	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56637800-56657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:56642600-56644400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:56642600-56644400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:56642600-56644600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:56642800-56644600	Enhancers	Cortex derived primary cultured neurospheres	brain

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