Variant report

Variant	rs73732121
Chromosome Location	chr5:1604373-1604374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10512659	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11133831	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11948870	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11951409	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11951807	1.00[ASN][1000 genomes]
rs11951980	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11952238	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11953233	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11954077	1.00[ASN][1000 genomes]
rs11955967	1.00[ASN][1000 genomes]
rs11957991	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11958097	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13165826	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2883372	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4415117	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864560	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55867519	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55957581	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56185279	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59610035	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59656356	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59806631	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61340395	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6867199	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6869310	1.00[ASN][1000 genomes]
rs6870117	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6871261	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6872202	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884318	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6888170	1.00[ASN][1000 genomes]
rs6888910	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6889629	0.93[AFR][1000 genomes];0.90[AMR][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	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717593	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717595	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717596	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717598	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717600	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73732122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732123	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73732124	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73732134	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7708447	1.00[ASN][1000 genomes]
rs7716004	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7725592	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728463	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728632	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729323	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7732756	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736524	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736669	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737033	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737331	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs73732121	SDHAP3	cis	Nerve Tibial	GTEx
rs73732121	SDHAP3	cis	Esophagus Mucosa	GTEx
rs73732121	SDHAP3	cis	Whole Blood	GTEx
rs73732121	SDHAP3	cis	Thyroid	GTEx
rs73732121	SDHAP3	cis	Esophagus Muscularis	GTEx
rs73732121	SDHAP3	cis	Artery Tibial	GTEx
rs73732121	RP11-43F13.1	cis	Whole Blood	GTEx
rs73732121	CTD-2012J19.3	cis	Esophagus Mucosa	GTEx

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

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	chr5:1595200-1608200	Weak transcription	Primary T cells from cord blood	blood
4	chr5:1595200-1610600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:1595200-1610600	Weak transcription	Aorta	Aorta
6	chr5:1595200-1610800	Weak transcription	Fetal Intestine Small	intestine
7	chr5:1595200-1610800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:1595200-1618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:1595200-1618400	Weak transcription	Liver	Liver
10	chr5:1595200-1618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:1595200-1618600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
13	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
14	chr5:1595400-1607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:1595400-1607400	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:1595400-1607800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:1595400-1608200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:1595400-1619200	Weak transcription	GM12878-XiMat	blood
19	chr5:1595400-1619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:1595600-1607400	Weak transcription	Fetal Lung	lung
25	chr5:1595800-1617200	Weak transcription	Thymus	Thymus
26	chr5:1597600-1607400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:1597600-1610600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:1597600-1612000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:1597600-1618800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:1597600-1619200	Weak transcription	Fetal Brain Female	brain
31	chr5:1597600-1621400	Weak transcription	Brain Substantia Nigra	brain
32	chr5:1597600-1621800	Weak transcription	Ovary	ovary
33	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
34	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:1600000-1607600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
40	chr5:1601600-1617200	Weak transcription	Fetal Intestine Large	intestine
41	chr5:1601600-1618000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:1601800-1606000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:1601800-1607400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:1601800-1616600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr5:1601800-1616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:1601800-1620600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:1602000-1606600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:1602000-1612000	Weak transcription	Dnd41	blood
49	chr5:1603800-1604600	Enhancers	Duodenum Mucosa	Duodenum
50	chr5:1604200-1607200	Weak transcription	Fetal Stomach	stomach

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