Variant report

Variant	rs7820396
Chromosome Location	chr8:54537782-54537783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10112441	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808882	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10958375	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10958376	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10958377	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958378	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958379	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958380	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958386	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778297	0.94[EUR][1000 genomes]
rs11779176	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779309	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11779641	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11785377	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11785465	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785489	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11987300	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11995715	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547226	0.86[ASN][1000 genomes]
rs12549885	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549903	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs12549929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12550388	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249182	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249232	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13251373	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13253006	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259310	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13260243	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266723	0.81[ASN][1000 genomes]
rs13268670	0.86[ASN][1000 genomes]
rs13274248	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13275215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382123	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1382125	0.86[ASN][1000 genomes]
rs1477960	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1477964	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1477965	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1477966	0.86[ASN][1000 genomes]
rs1551910	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1551911	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1551913	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035197	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2086071	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2086072	0.85[EUR][1000 genomes]
rs2086073	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2086074	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2086075	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2169693	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2199590	0.86[ASN][1000 genomes]
rs2199591	0.86[ASN][1000 genomes]
rs28376752	0.92[EUR][1000 genomes]
rs28521998	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28550710	0.86[EUR][1000 genomes]
rs3919868	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3940882	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4258030	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4531078	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4873261	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4873759	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62505102	0.82[EUR][1000 genomes]
rs6415668	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6415669	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6415672	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6415673	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6415674	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6415675	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473856	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6473860	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473862	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473863	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473864	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473865	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473866	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473867	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473868	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473870	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6473871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6473876	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66931312	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6983383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6989219	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6989676	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991676	0.86[ASN][1000 genomes]
rs6991825	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6996204	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7008144	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7009049	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7010314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7386091	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7386224	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7387992	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388189	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388300	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388337	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459503	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459559	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459598	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7460037	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7460923	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7460945	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7461003	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7461174	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7461405	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7461954	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7462195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7462612	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462881	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462940	0.86[ASN][1000 genomes]
rs7463378	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463478	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463499	0.86[EUR][1000 genomes]
rs7463519	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7464824	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465481	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465593	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465617	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465670	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825736	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7842388	0.86[ASN][1000 genomes]
rs9643813	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643814	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978137	0.86[ASN][1000 genomes]
rs978138	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs978139	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs978140	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979361	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758159	chr8:54474589-54737473	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2759616	chr8:54474589-54737473	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1813772	chr8:54520350-54540531	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	esv1830188	chr8:54520350-54601462	Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	nsv890919	chr8:54521248-54607336	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv1020081	chr8:54528266-54592073	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	nsv611381	chr8:54528760-54589344	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv3335953	chr8:54529448-54557707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv1030947	chr8:54535233-54592073	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7820396	SCN10A	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54532000-54538400	Weak transcription	Fetal Brain Male	brain
2	chr8:54537400-54544200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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