Variant report

Variant	rs12713962
Chromosome Location	chr2:78752270-78752271
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:78747682..78749204-chr2:78751235..78753165,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10169753	0.84[EUR][1000 genomes]
rs10170943	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs10171212	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172805	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs10172862	0.88[CHB][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10177943	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs10181596	0.92[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs10181697	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10185195	0.88[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10186398	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10189388	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10190509	0.96[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs10195905	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10198233	0.88[CHB][hapmap]
rs10209274	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs10209806	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10211110	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10445953	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865436	0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs11126671	0.85[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs11126675	0.94[CHB][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1158748	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1158749	0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1158750	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1158751	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1158752	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs11681421	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs11691001	0.94[CHB][hapmap]
rs11892778	0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12151438	0.94[CHB][hapmap]
rs12467896	0.93[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes]
rs12469848	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[TSI][hapmap]
rs12472183	0.94[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes]
rs12618295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621197	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713958	0.94[CHB][hapmap];0.93[CHD][hapmap]
rs12713963	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991119	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13382494	0.88[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes]
rs13382702	0.98[AFR][1000 genomes]
rs13408192	0.88[CHB][hapmap]
rs13427717	0.88[CHB][hapmap];0.97[CHD][hapmap];0.81[TSI][hapmap]
rs1356218	0.89[EUR][1000 genomes]
rs1402677	0.91[EUR][1000 genomes]
rs1402679	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs1402680	0.90[EUR][1000 genomes]
rs1402682	1.00[CHB][hapmap]
rs1516252	0.88[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap]
rs1516254	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap]
rs1521506	0.94[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes]
rs1521508	0.96[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs1554468	0.96[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs1554469	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs1554470	0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17643390	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17643432	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2861617	0.88[EUR][1000 genomes]
rs28852987	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567962	0.82[AFR][1000 genomes]
rs4638821	0.85[EUR][1000 genomes]
rs6547205	0.92[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs6547206	0.88[CHB][hapmap];1.00[CHD][hapmap]
rs66625308	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721050	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6735382	0.94[CHB][hapmap]
rs6761669	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs6761959	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7419388	0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7557459	0.94[CHB][hapmap]
rs7569472	0.88[EUR][1000 genomes]
rs7570801	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[TSI][hapmap]
rs7580939	0.94[CHB][hapmap];0.96[CHD][hapmap];0.81[TSI][hapmap]
rs7584934	0.80[AFR][1000 genomes]
rs7599677	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs7599820	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7602469	0.94[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes]
rs7606396	0.88[CHB][hapmap];0.97[CHD][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs967428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3584761	chr2:78545020-79430628	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998961	chr2:78574081-79150087	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1002687	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv535790	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv874362	chr2:78582650-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv428052	chr2:78615333-79075603	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874364	chr2:78640246-78857870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1007043	chr2:78653616-78796446	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv874365	chr2:78658280-78805852	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv874366	chr2:78658280-78857870	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv874367	chr2:78658280-78945755	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv874368	chr2:78668935-78805852	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv874369	chr2:78668935-78818453	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv874370	chr2:78668935-79013457	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1004668	chr2:78673888-78797459	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv535791	chr2:78673888-78797459	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1012656	chr2:78702064-78752270	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv874371	chr2:78714978-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv458396	chr2:78743121-78782764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	nsv582289	chr2:78743121-78782764	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12713962	PCGF1	cis	cerebellum	SCAN
rs12713962	POLE4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78750400-78752800	Weak transcription	HepG2	liver

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