Variant report

Variant	rs408076
Chromosome Location	chr5:111692850-111692851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1004383	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1004385	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10052915	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1019743	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1019744	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12519600	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474360	0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1962305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.99[ASN][1000 genomes]
rs1975017	0.86[ASN][1000 genomes]
rs2140625	0.89[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2140626	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2416283	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2416284	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs366217	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs366951	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs367807	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs368032	0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs370640	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs373303	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs373583	0.89[ASN][1000 genomes]
rs376395	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs378791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382482	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs387117	0.89[ASN][1000 genomes]
rs388091	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs402027	0.85[EUR][1000 genomes]
rs406359	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs406444	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs408127	0.81[ASN][1000 genomes]
rs424998	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429580	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs440759	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs441563	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs442777	0.84[ASN][1000 genomes]
rs442947	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs443024	0.89[ASN][1000 genomes]
rs447144	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4479888	0.96[ASN][1000 genomes]
rs454794	0.87[ASN][1000 genomes]
rs485823	0.86[EUR][1000 genomes]
rs4958040	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4958043	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61211890	0.81[EUR][1000 genomes]
rs6594591	0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6861186	0.86[ASN][1000 genomes]
rs6872155	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6877695	0.86[ASN][1000 genomes]
rs7711318	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7720180	0.85[ASN][1000 genomes]
rs7720546	0.85[ASN][1000 genomes]
rs7731169	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821733	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs821734	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs821735	0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs821745	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs987764	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs987765	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462386	chr5:111667572-111699317	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv599372	chr5:111667572-111699317	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs408076	SRP19	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111678600-111695600	Weak transcription	Pancreas	Pancrea
2	chr5:111684000-111702600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:111685200-111707000	Weak transcription	Ovary	ovary
4	chr5:111685200-111709800	Weak transcription	Aorta	Aorta
5	chr5:111685800-111693600	Weak transcription	Right Atrium	heart
6	chr5:111687200-111693600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:111689200-111702200	Weak transcription	Gastric	stomach
8	chr5:111689600-111693600	Weak transcription	Left Ventricle	heart
9	chr5:111689600-111708800	Weak transcription	Esophagus	oesophagus
10	chr5:111690400-111694200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:111691400-111694600	Weak transcription	Fetal Lung	lung
12	chr5:111691800-111694600	Enhancers	Fetal Heart	heart
13	chr5:111692000-111693800	Enhancers	Right Ventricle	heart

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