Variant report

Variant	rs11679986
Chromosome Location	chr2:113044101-113044102
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	chr2:113031677..113034717-chr2:113042895..113047019,4	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10864901	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11123133	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11676628	0.85[EUR][1000 genomes]
rs11682795	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11685462	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11685514	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11687980	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11688511	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11689858	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11691239	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11693294	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11695974	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12474447	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12477879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4516428	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55798617	0.95[EUR][1000 genomes]
rs55802705	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55821286	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55861985	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56044884	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56048537	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711180	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6722612	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6747639	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6759283	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6761440	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831633	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831634	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831636	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831638	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831639	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72831641	0.87[EUR][1000 genomes]
rs72831642	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72831649	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831651	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831658	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831660	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831662	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831664	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72831685	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831688	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72833410	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833412	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833413	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833414	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833415	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833428	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833432	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586893	0.83[EUR][1000 genomes]
rs7587316	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7596661	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7599551	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
6	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
7	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv963704	chr2:113036252-113044944	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv874875	chr2:113038409-113070889	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1821302	chr2:113041461-113053061	Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3460331	chr2:113043881-113048279	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3460332	chr2:113043881-113048279	Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11679986	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11679986	RGPD8	cis	Nerve Tibial	GTEx
rs11679986	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11679986	RGPD8	cis	Muscle Skeletal	GTEx
rs11679986	RGPD8	cis	Thyroid	GTEx
rs11679986	RGPD8	cis	Esophagus Mucosa	GTEx
rs11679986	ZC3H8	cis	Artery Tibial	GTEx
rs11679986	RGPD8	cis	Heart Left Ventricle	GTEx
rs11679986	RGPD8	cis	Adipose Subcutaneous	GTEx
rs11679986	RGPD8	cis	Artery Aorta	GTEx
rs11679986	RGPD8	cis	Esophagus Muscularis	GTEx
rs11679986	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs11679986	RGPD8	cis	Whole Blood	GTEx
rs11679986	RGPD8	cis	Artery Tibial	GTEx
rs11679986	RGPD8	cis	lung	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034200-113058200	Weak transcription	Ovary	ovary
2	chr2:113034400-113047800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:113034400-113051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
5	chr2:113035000-113046000	Weak transcription	Fetal Kidney	kidney
6	chr2:113035000-113057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:113035000-113057800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:113035000-113057800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:113035400-113047600	Weak transcription	Osteobl	bone
10	chr2:113035600-113047600	Weak transcription	NHDF-Ad	bronchial
11	chr2:113035600-113058200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:113035800-113058000	Weak transcription	Primary T cells from cord blood	blood
13	chr2:113035800-113060400	Weak transcription	Fetal Thymus	thymus
14	chr2:113035800-113067400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:113036600-113058000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:113037000-113054200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:113040000-113081800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:113040600-113054400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:113041200-113058600	Weak transcription	Fetal Heart	heart
20	chr2:113041400-113058600	Weak transcription	K562	blood
21	chr2:113041800-113047800	Weak transcription	Liver	Liver
22	chr2:113042400-113051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:113042600-113047600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:113043000-113044200	Enhancers	Pancreas	Pancrea

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