Variant report

Variant	rs10261458
Chromosome Location	chr7:146780248-146780249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EZH2-4	chr7:146779632-146780313	ENSG00000236795.1

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1014686	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10231780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10256502	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10256846	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10258525	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10260427	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10268697	0.91[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272523	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10275671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10952669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12666908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1548743	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1860478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1860479	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2159473	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2191272	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2191273	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464781	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6464782	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6464783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6975159	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs740809	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs740810	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs740811	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7777531	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7802708	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809722	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9640233	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9640234	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1021251	chr7:146522341-146802125	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029646	chr7:146702080-146788213	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1015266	chr7:146707047-146788213	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2761380	chr7:146707059-146788225	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1034510	chr7:146719973-146848581	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv933033	chr7:146720301-147081560	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1033898	chr7:146721499-147081768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv931005	chr7:146730472-147381257	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
9	nsv933740	chr7:146762650-146783928	Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	nsv933628	chr7:146762650-146794398	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	esv3324600	chr7:146779869-146782967	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	n/a
12	esv3443301	chr7:146780044-146782892	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10261458	GIMAP8	cis	parietal	SCAN
rs10261458	ZNF746	cis	parietal	SCAN
rs10261458	ACTR3C	cis	parietal	SCAN
rs10261458	LACRT	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:146777200-146780400	Enhancers	Fetal Brain Male	brain
2	chr7:146779200-146782400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:146779600-146781400	Weak transcription	Stomach Mucosa	stomach
4	chr7:146780200-146780400	Enhancers	Pancreas	Pancrea

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