Variant report

Variant	rs10805671
Chromosome Location	chr5:43271547-43271548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43268161..43270629-chr5:43271239..43274224,3	K562	blood:
2	chr5:43271201..43273995-chr5:43287069..43290020,2	K562	blood:

Variant related genes	Relation type
ENSG00000261604	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10039048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10039617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10065852	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10462047	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10462048	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10512825	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10512827	0.89[CEU][hapmap];0.83[MEX][hapmap]
rs10512828	0.89[CEU][hapmap]
rs10805672	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10805673	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10805674	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10805675	0.89[CEU][hapmap]
rs10941620	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10941621	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10941622	0.81[EUR][1000 genomes]
rs10941623	0.81[EUR][1000 genomes]
rs10941630	0.92[CEU][hapmap]
rs10941631	0.89[CEU][hapmap]
rs11739009	0.92[CEU][hapmap]
rs11739665	0.81[EUR][1000 genomes]
rs11740128	0.92[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs11741246	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs11742171	0.92[CEU][hapmap]
rs11742712	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs11743622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11743633	0.92[CEU][hapmap]
rs11746629	0.89[EUR][1000 genomes]
rs11950040	0.89[CEU][hapmap]
rs11950448	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs11956635	0.89[CEU][hapmap]
rs11956988	0.88[CEU][hapmap]
rs12514393	0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs12514399	0.92[CEU][hapmap]
rs12515072	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12518032	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12518127	0.89[CEU][hapmap]
rs12519554	0.92[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs12520012	0.81[EUR][1000 genomes]
rs13659	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1545753	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1548097	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1564196	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs1564197	0.92[CEU][hapmap]
rs1564198	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17244818	0.92[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2086133	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126948	0.92[CEU][hapmap]
rs2126949	0.91[CEU][hapmap]
rs2330150	0.81[EUR][1000 genomes]
rs35231094	0.89[EUR][1000 genomes]
rs35239179	0.81[EUR][1000 genomes]
rs3733768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3733769	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4254917	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4288122	0.92[CEU][hapmap]
rs4373285	0.81[EUR][1000 genomes]
rs4395639	0.92[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4443426	0.96[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs4866734	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4866738	0.92[CEU][hapmap]
rs4866741	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4866813	0.81[EUR][1000 genomes]
rs4866818	0.92[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4866820	0.96[CEU][hapmap]
rs4866822	0.92[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs4866824	0.96[CEU][hapmap]
rs4866826	0.81[EUR][1000 genomes]
rs55647314	0.83[EUR][1000 genomes]
rs55794239	0.82[EUR][1000 genomes]
rs55800451	0.85[EUR][1000 genomes]
rs56023994	0.84[EUR][1000 genomes]
rs56029402	0.85[EUR][1000 genomes]
rs56114604	0.81[EUR][1000 genomes]
rs57392430	0.85[EUR][1000 genomes]
rs60207549	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66585077	0.89[EUR][1000 genomes]
rs66691321	0.81[EUR][1000 genomes]
rs67415672	0.84[EUR][1000 genomes]
rs6814	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6863360	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6886499	0.85[CEU][hapmap]
rs6887351	0.92[CEU][hapmap]
rs6895805	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6898398	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs754527	0.93[CHB][hapmap]
rs7701391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7701642	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs7704588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7708779	0.92[CEU][hapmap]
rs7714027	0.89[CEU][hapmap]
rs7714919	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7716091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7720165	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7720681	0.89[CEU][hapmap]
rs7722781	0.81[EUR][1000 genomes]
rs7727047	0.85[CEU][hapmap]
rs7734293	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs9292871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9292874	0.80[EUR][1000 genomes]
rs9790987	0.92[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
4	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10805671	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs10805671	HMGCS1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43246600-43281400	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:43257400-43274400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:43269000-43273000	Weak transcription	GM12878-XiMat	blood
4	chr5:43270200-43277400	Weak transcription	Brain Angular Gyrus	brain
5	chr5:43271200-43273600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:43271200-43280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:43271400-43273800	Weak transcription	NHEK	skin

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