Variant report

Variant	rs9427662
Chromosome Location	chr1:196946775-196946776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1034162	0.86[EUR][1000 genomes]
rs10429911	0.87[CEU][hapmap]
rs10732295	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs10732296	0.87[CEU][hapmap]
rs10733087	0.86[EUR][1000 genomes]
rs10754213	0.86[EUR][1000 genomes]
rs10754214	0.86[EUR][1000 genomes]
rs10754215	0.86[EUR][1000 genomes]
rs10801587	0.86[EUR][1000 genomes]
rs10801588	0.86[EUR][1000 genomes]
rs10801590	0.86[EUR][1000 genomes]
rs10801591	0.86[EUR][1000 genomes]
rs10922165	0.84[EUR][1000 genomes]
rs10922166	0.86[EUR][1000 genomes]
rs1115246	0.81[EUR][1000 genomes]
rs1115247	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1170878	1.00[EUR][1000 genomes]
rs1170880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1170881	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1170882	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1170883	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12039586	0.86[EUR][1000 genomes]
rs12092294	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12677	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12731209	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1332662	1.00[CEU][hapmap]
rs1332663	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs1332669	0.89[EUR][1000 genomes]
rs1412631	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1412632	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1412633	0.86[EUR][1000 genomes]
rs1412634	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1412639	0.89[EUR][1000 genomes]
rs1537319	0.86[EUR][1000 genomes]
rs1571964	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs1576878	0.89[EUR][1000 genomes]
rs1627765	0.86[EUR][1000 genomes]
rs1759006	0.86[EUR][1000 genomes]
rs1759007	0.86[EUR][1000 genomes]
rs1759008	0.86[EUR][1000 genomes]
rs1759009	0.86[EUR][1000 genomes]
rs1759013	0.86[EUR][1000 genomes]
rs1794003	0.86[EUR][1000 genomes]
rs1794010	0.86[EUR][1000 genomes]
rs1855116	1.00[EUR][1000 genomes]
rs1888991	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs1953064	0.86[EUR][1000 genomes]
rs2026429	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2151133	0.86[EUR][1000 genomes]
rs2151134	1.00[CEU][hapmap]
rs2336595	0.89[EUR][1000 genomes]
rs2336597	0.89[EUR][1000 genomes]
rs34650634	0.88[AMR][1000 genomes]
rs3891964	0.86[EUR][1000 genomes]
rs4342879	0.87[CEU][hapmap]
rs4350226	0.87[CEU][hapmap]
rs4915148	0.86[EUR][1000 genomes]
rs4915156	0.86[EUR][1000 genomes]
rs4915313	0.86[EUR][1000 genomes]
rs4915315	0.86[EUR][1000 genomes]
rs4915316	0.86[EUR][1000 genomes]
rs4915327	0.86[EUR][1000 genomes]
rs4915337	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs5997	0.86[EUR][1000 genomes]
rs6003	0.86[EUR][1000 genomes]
rs6428387	0.86[EUR][1000 genomes]
rs6656448	0.85[CEU][hapmap]
rs6656858	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs6657171	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6657246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671696	0.86[EUR][1000 genomes]
rs6677082	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6680497	0.86[EUR][1000 genomes]
rs6685259	0.86[EUR][1000 genomes]
rs6692162	0.83[AFR][1000 genomes]
rs6694672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702340	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6703400	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7411719	0.86[EUR][1000 genomes]
rs7534353	1.00[CEU][hapmap]
rs7539642	0.86[EUR][1000 genomes]
rs7542397	1.00[CEU][hapmap]
rs7554757	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs857017	0.89[EUR][1000 genomes]
rs857020	0.86[EUR][1000 genomes]
rs857021	0.89[EUR][1000 genomes]
rs857022	0.89[EUR][1000 genomes]
rs857023	0.89[EUR][1000 genomes]
rs857026	0.89[EUR][1000 genomes]
rs857027	0.89[EUR][1000 genomes]
rs865071	0.87[EUR][1000 genomes]
rs877897	1.00[CEU][hapmap]
rs928439	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs928440	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9427660	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9427661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9427942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757766	chr1:196590837-196961802	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv428290	chr1:196590837-196961802	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv471614	chr1:196669511-196955230	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv1806946	chr1:196673954-196974876	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv933234	chr1:196706651-196946907	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	esv2756880	chr1:196709223-197066074	ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	esv2750822	chr1:196731148-196993973	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv430124	chr1:196731148-196993973	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv34978	chr1:196733133-197011577	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv430158	chr1:196733133-197011577	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv430180	chr1:196739837-197007479	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv469599	chr1:196796476-196955230	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv482699	chr1:196796476-196955230	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1003814	chr1:196825211-196982487	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1003573	chr1:196825211-197005106	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv524689	chr1:196941493-196946775	Flanking Active TSS Active TSS Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
20	nsv8702	chr1:196943852-196954575	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196945600-196949200	Active TSS	Liver	Liver
2	chr1:196946600-196947000	Enhancers	HepG2	liver

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