Variant report

Variant	rs2389519
Chromosome Location	chr4:119009752-119009753
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 186 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs10008049	0.95[ASN][1000 genomes]
rs10014096	0.94[ASN][1000 genomes]
rs10015232	0.95[ASN][1000 genomes]
rs10016285	0.95[ASN][1000 genomes]
rs10020473	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10021128	0.94[ASN][1000 genomes]
rs10021781	0.95[ASN][1000 genomes]
rs10023699	0.95[ASN][1000 genomes]
rs10026541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10027013	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10027893	0.94[ASN][1000 genomes]
rs10033308	0.91[ASN][1000 genomes]
rs10033412	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10440400	0.95[ASN][1000 genomes]
rs11098421	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11098422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098424	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098427	0.95[ASN][1000 genomes]
rs11098428	0.95[ASN][1000 genomes]
rs11722962	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11728724	0.94[ASN][1000 genomes]
rs11730541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730611	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11733562	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11736688	0.91[ASN][1000 genomes]
rs11937777	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11947071	0.93[ASN][1000 genomes]
rs12499751	0.94[ASN][1000 genomes]
rs12505156	0.90[ASN][1000 genomes]
rs12505642	0.81[AMR][1000 genomes]
rs12508017	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12711064	0.95[ASN][1000 genomes]
rs13104129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13111697	0.95[ASN][1000 genomes]
rs13114621	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13114895	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125397	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13126882	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13127321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13134901	0.95[ASN][1000 genomes]
rs13135646	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13137083	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13139875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1319938	0.97[ASN][1000 genomes]
rs1872771	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1994384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049362	0.90[ASN][1000 genomes]
rs2140475	0.88[ASN][1000 genomes]
rs2254215	0.81[GIH][hapmap]
rs2254218	0.81[GIH][hapmap]
rs2389500	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2389501	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2389503	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2389509	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2389510	0.85[CHB][hapmap];0.94[ASN][1000 genomes]
rs2389511	0.94[ASN][1000 genomes]
rs2389512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389513	0.98[ASN][1000 genomes]
rs2389514	0.98[ASN][1000 genomes]
rs2389515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389517	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389518	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389523	0.99[ASN][1000 genomes]
rs2389524	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389525	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389526	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389527	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2892785	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2892786	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2892787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2892788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2892789	0.99[ASN][1000 genomes]
rs2892790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2892791	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2892799	0.89[ASN][1000 genomes]
rs4131600	0.95[ASN][1000 genomes]
rs4240313	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4240314	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4240316	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240317	0.97[ASN][1000 genomes]
rs4240318	0.97[ASN][1000 genomes]
rs4280816	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4397073	0.95[ASN][1000 genomes]
rs4437319	0.94[ASN][1000 genomes]
rs4452509	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4546313	0.86[ASN][1000 genomes]
rs4558930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4566725	0.97[ASN][1000 genomes]
rs4569819	0.97[ASN][1000 genomes]
rs4576085	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4616829	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833560	0.95[ASN][1000 genomes]
rs4833561	0.95[ASN][1000 genomes]
rs4833563	0.95[ASN][1000 genomes]
rs4833566	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4833567	0.86[ASN][1000 genomes]
rs4834656	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834657	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834658	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4834660	0.95[ASN][1000 genomes]
rs4834661	0.95[ASN][1000 genomes]
rs4834664	0.95[ASN][1000 genomes]
rs4834665	0.95[ASN][1000 genomes]
rs4834666	0.91[ASN][1000 genomes]
rs581739	0.85[ASN][1000 genomes]
rs582448	0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs586073	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs586224	0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs593966	0.85[ASN][1000 genomes]
rs597881	0.85[ASN][1000 genomes]
rs607961	0.86[ASN][1000 genomes]
rs608228	0.84[ASN][1000 genomes]
rs610222	0.82[ASN][1000 genomes]
rs613083	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs613443	0.85[ASN][1000 genomes]
rs615837	0.82[ASN][1000 genomes]
rs617140	0.84[ASN][1000 genomes]
rs62328865	0.85[ASN][1000 genomes]
rs62328871	0.84[ASN][1000 genomes]
rs625546	0.83[ASN][1000 genomes]
rs627249	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs641962	0.85[ASN][1000 genomes]
rs6534078	0.81[GIH][hapmap]
rs6534082	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662086	0.85[ASN][1000 genomes]
rs674514	0.83[ASN][1000 genomes]
rs678177	0.86[ASN][1000 genomes]
rs6816778	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6818042	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6820061	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820108	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6823125	0.95[ASN][1000 genomes]
rs6823295	0.95[ASN][1000 genomes]
rs6825105	0.97[ASN][1000 genomes]
rs6828552	0.95[ASN][1000 genomes]
rs6837896	0.90[ASN][1000 genomes]
rs6842393	0.93[ASN][1000 genomes]
rs6842557	0.81[ASN][1000 genomes]
rs6842719	0.84[ASN][1000 genomes]
rs6848037	0.97[ASN][1000 genomes]
rs6848598	0.97[ASN][1000 genomes]
rs6851494	0.94[ASN][1000 genomes]
rs6857041	0.95[ASN][1000 genomes]
rs6857232	0.95[ASN][1000 genomes]
rs7435948	0.95[ASN][1000 genomes]
rs7439663	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7655439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7671232	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671359	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671434	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7671515	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671562	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679658	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7685325	0.95[ASN][1000 genomes]
rs7686670	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687849	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7688063	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7688443	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7695706	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699653	0.83[ASN][1000 genomes]
rs788647	0.82[ASN][1000 genomes]
rs788650	0.82[ASN][1000 genomes]
rs788651	0.82[ASN][1000 genomes]
rs788655	0.82[ASN][1000 genomes]
rs788661	0.84[ASN][1000 genomes]
rs788662	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs788668	0.84[ASN][1000 genomes]
rs9307452	0.95[ASN][1000 genomes]
rs9637622	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9637623	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790637	0.97[ASN][1000 genomes]
rs9995675	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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 target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879839	chr4:118967196-119010126	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv1008236	chr4:118989467-119154024	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv999152	chr4:119001143-119138322	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2389519	SEC24D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119008800-119013800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119009000-119011200	Strong transcription	Dnd41	blood
3	chr4:119009200-119013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:119009600-119009800	Enhancers	H9 Cell Line	embryonic stem cell

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