Variant report

Variant	rs17712820
Chromosome Location	chr5:57879427-57879428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10071783	0.87[CHB][hapmap]
rs11742549	0.83[CEU][hapmap]
rs11745321	0.87[CHB][hapmap]
rs11955748	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152846	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422230	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1605741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1605742	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs17712683	1.00[CEU][hapmap]
rs2307117	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs35454977	1.00[ASN][1000 genomes]
rs4551014	0.87[CHB][hapmap]
rs60365444	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60630307	1.00[ASN][1000 genomes]
rs62367812	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367813	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367814	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62367815	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367816	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62367842	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367844	1.00[ASN][1000 genomes]
rs6865094	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6890117	0.87[CHB][hapmap]
rs6890362	0.87[CHB][hapmap]
rs6891534	0.87[CHB][hapmap]
rs6895777	0.87[CHB][hapmap]
rs6895889	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6896790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7723416	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17712820	GAPT	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57877400-57880000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr5:57877600-57879600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr5:57877600-57879600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:57877600-57880000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:57877600-57880000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:57877600-57880400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:57877800-57879600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:57877800-57879600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:57877800-57879600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:57877800-57879600	Flanking Active TSS	Right Ventricle	heart
11	chr5:57877800-57879600	Enhancers	Spleen	Spleen
12	chr5:57877800-57879800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:57878000-57879600	Flanking Active TSS	Liver	Liver
14	chr5:57878200-57879600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:57878200-57880400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr5:57878400-57879600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:57878400-57879600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
18	chr5:57878400-57879800	Active TSS	Fetal Brain Male	brain
19	chr5:57878400-57880000	Active TSS	Brain Hippocampus Middle	brain
20	chr5:57878400-57880400	Active TSS	Brain Cingulate Gyrus	brain
21	chr5:57878600-57879600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:57878600-57879800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr5:57878800-57879600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
24	chr5:57878800-57879600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr5:57878800-57879600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:57879000-57879600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr5:57879000-57879600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:57879000-57879600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr5:57879000-57879600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:57879000-57879600	Flanking Active TSS	Pancreas	Pancrea
31	chr5:57879000-57879600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr5:57879000-57879800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:57879200-57879600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
34	chr5:57879200-57879600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:57879200-57879600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:57879200-57879600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr5:57879200-57879600	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr5:57879200-57879600	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr5:57879200-57879600	Flanking Bivalent TSS/Enh	A549	lung
40	chr5:57879200-57879800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr5:57879200-57879800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:57879200-57879800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:57879200-57879800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:57879200-57879800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr5:57879200-57879800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr5:57879200-57879800	Bivalent/Poised TSS	Fetal Stomach	stomach
47	chr5:57879200-57880000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
48	chr5:57879200-57880000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr5:57879200-57880000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:57879200-57880000	Bivalent/Poised TSS	Fetal Kidney	kidney

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