Variant report

Variant	rs72831664
Chromosome Location	chr2:113008633-113008634
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112995119..113002036-chr2:113006971..113012595,10	K562	blood:
2	chr2:112640166..112643875-chr2:113008551..113014158,5	K562	blood:
3	chr2:113006375..113009126-chr2:113033246..113034837,2	K562	blood:
4	chr2:113008180..113009810-chr2:113032329..113034455,2	K562	blood:
5	chr2:112998287..113000256-chr2:113007615..113010279,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000153107	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10864901	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123133	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676628	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11679986	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11682795	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11685462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11685514	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687980	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11688511	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11689858	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11691239	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693294	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12474447	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12477879	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4516428	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55798617	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55802705	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55821286	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55861985	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56044884	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56048537	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6711180	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6722612	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6731628	0.87[AFR][1000 genomes]
rs6747639	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759283	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6761440	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831633	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831634	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831636	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831638	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831639	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72831641	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72831642	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831649	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831651	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831658	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831660	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831685	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831688	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72833410	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833412	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833413	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833414	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833415	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833428	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72833431	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72833432	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7586893	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7587316	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7596661	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7599551	0.88[AMR][1000 genomes];0.96[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	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	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
7	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
8	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs72831664	RGPD8	cis	Esophagus Muscularis	GTEx
rs72831664	RGPD8	cis	Esophagus Mucosa	GTEx
rs72831664	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72831664	RGPD8	cis	lung	GTEx
rs72831664	RGPD8	cis	Thyroid	GTEx
rs72831664	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72831664	RGPD8	cis	Muscle Skeletal	GTEx
rs72831664	RGPD8	cis	Nerve Tibial	GTEx
rs72831664	RGPD8	cis	Heart Left Ventricle	GTEx
rs72831664	RGPD8	cis	Artery Tibial	GTEx
rs72831664	RGPD8	cis	Artery Aorta	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
3	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
4	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
5	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
8	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
9	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
13	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:112980000-113011800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:112980200-113011600	Weak transcription	HSMM	muscle
16	chr2:112987200-113010800	Weak transcription	NH-A	brain
17	chr2:112987200-113011000	Weak transcription	NHDF-Ad	bronchial
18	chr2:112987400-113011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:112987800-113011000	Weak transcription	NHEK	skin
20	chr2:112987800-113011800	Weak transcription	NHLF	lung
21	chr2:112988400-113011600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:112990800-113009200	Weak transcription	Hela-S3	cervix
23	chr2:112992200-113011400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:112992200-113011800	Weak transcription	HSMMtube	muscle
25	chr2:112993000-113011000	Weak transcription	HMEC	breast
26	chr2:112993400-113011000	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:112994600-113008800	Weak transcription	Spleen	Spleen
28	chr2:112994600-113011800	Weak transcription	Colonic Mucosa	Colon
29	chr2:112999800-113008800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:113000800-113009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:113000800-113009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:113001200-113011400	Weak transcription	HUVEC	blood vessel
33	chr2:113004000-113009000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:113004000-113009800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:113004200-113009200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:113004200-113010200	Weak transcription	Fetal Brain Male	brain
37	chr2:113004200-113011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:113004400-113011400	Weak transcription	Fetal Heart	heart
39	chr2:113004400-113011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:113004400-113011800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:113004400-113012000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:113004600-113011400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:113005200-113011400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:113005600-113008800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:113005600-113009000	Weak transcription	Osteobl	bone
46	chr2:113005600-113011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:113005600-113011400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:113005600-113011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:113005600-113011400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:113005600-113011400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links