Variant report

Variant	rs6761440
Chromosome Location	chr2:112959193-112959194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112951422..112953585-chr2:112957431..112959330,2	K562	blood:
2	chr2:112958985..112961964-chr2:112963892..112966178,2	K562	blood:
3	chr2:112953778..112955345-chr2:112957408..112960212,2	K562	blood:
4	chr2:112950076..112953760-chr2:112955704..112959330,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10864901	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123130	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11123133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11676628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679986	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11682795	0.91[AMR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685514	0.91[AMR][1000 genomes]
rs11687980	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11688511	0.84[AMR][1000 genomes]
rs11689858	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11691239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693294	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11695974	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11903915	1.00[ASN][1000 genomes]
rs12474447	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12711736	0.89[ASN][1000 genomes]
rs4516428	0.84[AMR][1000 genomes]
rs4848281	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4849051	0.89[ASN][1000 genomes]
rs55798617	0.86[EUR][1000 genomes]
rs55802705	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55861985	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56048537	0.84[AMR][1000 genomes]
rs6708607	1.00[ASN][1000 genomes]
rs6711180	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6722612	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831641	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831651	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831658	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831662	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831664	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831685	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72833412	0.84[AMR][1000 genomes]
rs72833413	0.84[AMR][1000 genomes]
rs72833414	0.91[AMR][1000 genomes]
rs72833415	0.84[AMR][1000 genomes]
rs72833428	0.84[AMR][1000 genomes]
rs72833432	0.84[AMR][1000 genomes]
rs7586893	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7587316	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7596661	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7599551	0.96[AMR][1000 genomes];0.89[EUR][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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6761440	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6761440	RGPD8	cis	Artery Aorta	GTEx
rs6761440	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6761440	RGPD8	cis	Nerve Tibial	GTEx
rs6761440	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs6761440	RGPD8	cis	Thyroid	GTEx
rs6761440	RGPD8	cis	Artery Tibial	GTEx
rs6761440	RGPD8	cis	lung	GTEx
rs6761440	RGPD8	cis	Heart Left Ventricle	GTEx
rs6761440	RGPD8	cis	Muscle Skeletal	GTEx
rs6761440	RGPD8	cis	Esophagus Mucosa	GTEx
rs6761440	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6761440	RGPD8	cis	Whole Blood	GTEx
rs6761440	RGPD8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
3	chr2:112952800-112960200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:112953200-112960400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:112953800-112960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:112953800-112960400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:112953800-112960400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:112953800-112960800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:112953800-112961600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:112958400-112959600	Enhancers	Primary T cells from cord blood	blood
11	chr2:112958400-112959600	Enhancers	HUVEC	blood vessel
12	chr2:112958600-112959200	Enhancers	Fetal Thymus	thymus
13	chr2:112959000-112959400	Enhancers	Stomach Mucosa	stomach
14	chr2:112959000-112959800	Enhancers	Liver	Liver

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