Variant report

Variant	rs11953233
Chromosome Location	chr5:1617447-1617448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10512659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11133831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951807	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954077	1.00[ASN][1000 genomes]
rs11955967	1.00[ASN][1000 genomes]
rs11957991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165826	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2883372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415117	1.00[ASN][1000 genomes]
rs55864560	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55867519	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957581	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185279	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58452381	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58687576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59610035	1.00[ASN][1000 genomes]
rs59656356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59806631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340395	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869310	1.00[ASN][1000 genomes]
rs6870117	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6871261	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6872202	1.00[ASN][1000 genomes]
rs6884318	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888170	1.00[ASN][1000 genomes]
rs6888910	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889629	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889684	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	1.00[ASN][1000 genomes]
rs72717589	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732121	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73732122	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73732123	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73732124	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73732134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708447	1.00[ASN][1000 genomes]
rs7716004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725592	1.00[ASN][1000 genomes]
rs7728463	1.00[ASN][1000 genomes]
rs7728632	1.00[ASN][1000 genomes]
rs7729323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732756	1.00[ASN][1000 genomes]
rs7736524	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736669	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737033	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737331	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers 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	29 gene(s)	inside rSNPs	diseases
7	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11953233	SDHAP3	cis	Esophagus Muscularis	GTEx
rs11953233	SDHAP3	cis	Nerve Tibial	GTEx
rs11953233	CTD-2012J19.3	cis	Esophagus Mucosa	GTEx
rs11953233	SDHAP3	cis	Whole Blood	GTEx
rs11953233	SDHAP3	cis	Esophagus Mucosa	GTEx
rs11953233	SDHAP3	cis	Thyroid	GTEx
rs11953233	SDHAP3	cis	Artery Tibial	GTEx
rs11953233	RP11-43F13.1	cis	Whole Blood	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
3	chr5:1595200-1618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:1595200-1618400	Weak transcription	Liver	Liver
5	chr5:1595200-1618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:1595200-1618600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
8	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
9	chr5:1595400-1619200	Weak transcription	GM12878-XiMat	blood
10	chr5:1595400-1619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
12	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:1597600-1618800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:1597600-1619200	Weak transcription	Fetal Brain Female	brain
17	chr5:1597600-1621400	Weak transcription	Brain Substantia Nigra	brain
18	chr5:1597600-1621800	Weak transcription	Ovary	ovary
19	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
20	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
25	chr5:1601600-1618000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:1601800-1620600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:1606200-1633200	Weak transcription	Brain Anterior Caudate	brain
28	chr5:1607200-1618400	Weak transcription	Lung	lung
29	chr5:1607600-1621000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:1607600-1626600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:1607800-1623800	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:1608000-1620600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:1608000-1624200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:1608200-1619000	Weak transcription	Right Atrium	heart
35	chr5:1608400-1626400	Weak transcription	Pancreas	Pancrea
36	chr5:1608600-1620800	Weak transcription	Brain Germinal Matrix	brain
37	chr5:1608800-1624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:1608800-1632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:1608800-1633800	Weak transcription	Fetal Lung	lung
40	chr5:1609200-1633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:1609200-1633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:1609400-1618600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:1609400-1619200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:1609400-1619400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:1609600-1619000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:1609600-1633600	Weak transcription	Left Ventricle	heart
47	chr5:1609800-1626400	Weak transcription	HepG2	liver
48	chr5:1610000-1621600	Weak transcription	Fetal Kidney	kidney
49	chr5:1610000-1624400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:1610000-1633400	Weak transcription	Colonic Mucosa	Colon

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