Variant report

Variant	rs7599809
Chromosome Location	chr2:142139756-142139757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10208014	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1033315	0.95[JPT][hapmap]
rs10803483	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1121374	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs11692778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694011	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]
rs11886555	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12052880	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12469827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12691601	0.95[ASN][1000 genomes]
rs12691602	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16845984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2683824	0.86[LWK][hapmap]
rs2683829	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs2683866	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2683870	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2714174	0.86[LWK][hapmap]
rs2714177	0.86[LWK][hapmap]
rs2714179	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2714212	0.86[LWK][hapmap]
rs4245855	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4404210	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4622649	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55954502	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165750	0.95[ASN][1000 genomes]
rs7560169	0.80[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs975607	0.91[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583198	chr2:141510791-142150620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1009434	chr2:141832339-142156180	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
4	esv2830111	chr2:142047759-142164422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3693337	chr2:142047759-142164422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2757835	chr2:142071391-142217569	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2759095	chr2:142071391-142245947	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv875231	chr2:142113241-142156180	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv875232	chr2:142113241-142172366	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
11	esv2830236	chr2:142125733-142151405	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
12	nsv522203	chr2:142134134-142141415	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7599809	SPOPL	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142138400-142143200	Enhancers	Dnd41	blood
2	chr2:142139600-142139800	Enhancers	Brain Anterior Caudate	brain
3	chr2:142139600-142140000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:142139600-142140200	Enhancers	Brain Inferior Temporal Lobe	brain

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