Variant report

Variant	rs7708447
Chromosome Location	chr5:1592286-1592287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1592112-1592357	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:1592104-1592475	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:1592115-1592347	GM12878	blood:	n/a	n/a
4	TCF3	chr5:1592131-1592452	GM12878	blood:	n/a	chr5:1592139-1592148
5	POLR2A	chr5:1591635-1592503	GM12892	blood:	n/a	n/a
6	PBX3	chr5:1592282-1592450	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:1592151-1592354	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:1591770-1592551	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:1592279-1592365	K562	blood:	n/a	n/a
10	POLR2A	chr5:1592162-1592392	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000271119	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11133831	1.00[ASN][1000 genomes]
rs11948870	1.00[ASN][1000 genomes]
rs11951409	1.00[ASN][1000 genomes]
rs11951807	1.00[ASN][1000 genomes]
rs11951980	1.00[ASN][1000 genomes]
rs11952238	1.00[ASN][1000 genomes]
rs11953233	1.00[ASN][1000 genomes]
rs11954077	1.00[ASN][1000 genomes]
rs11955967	1.00[ASN][1000 genomes]
rs11957991	1.00[ASN][1000 genomes]
rs11958097	1.00[ASN][1000 genomes]
rs2883372	1.00[ASN][1000 genomes]
rs4415117	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864560	1.00[ASN][1000 genomes]
rs55867519	1.00[ASN][1000 genomes]
rs55957581	1.00[ASN][1000 genomes]
rs56185279	1.00[ASN][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	1.00[ASN][1000 genomes]
rs59610035	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59656356	1.00[ASN][1000 genomes]
rs59806631	1.00[ASN][1000 genomes]
rs61340395	1.00[ASN][1000 genomes]
rs6867199	1.00[ASN][1000 genomes]
rs6869310	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6870117	1.00[ASN][1000 genomes]
rs6871261	1.00[ASN][1000 genomes]
rs6872202	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884318	1.00[ASN][1000 genomes]
rs6888170	1.00[ASN][1000 genomes]
rs6888910	1.00[ASN][1000 genomes]
rs6889629	1.00[ASN][1000 genomes]
rs6889684	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717589	1.00[ASN][1000 genomes]
rs72717593	1.00[ASN][1000 genomes]
rs72717595	1.00[ASN][1000 genomes]
rs72717596	1.00[ASN][1000 genomes]
rs72717598	1.00[ASN][1000 genomes]
rs72717600	1.00[ASN][1000 genomes]
rs73732121	1.00[ASN][1000 genomes]
rs73732122	1.00[ASN][1000 genomes]
rs73732124	1.00[ASN][1000 genomes]
rs73732134	1.00[ASN][1000 genomes]
rs7716004	1.00[ASN][1000 genomes]
rs7725592	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728463	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728632	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729323	1.00[ASN][1000 genomes]
rs7732756	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736524	1.00[ASN][1000 genomes]
rs7736669	1.00[ASN][1000 genomes]
rs7737033	1.00[ASN][1000 genomes]
rs7737331	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881664	chr5:1377172-1594879	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	nsv880471	chr5:1466813-1598468	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv881644	chr5:1478021-1597272	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv881574	chr5:1537141-1598468	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	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
12	nsv881282	chr5:1549771-1597272	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	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
14	esv3418475	chr5:1590952-1594050	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv3429404	chr5:1590952-1594050	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7708447	SDHAP3	cis	Whole Blood	GTEx
rs7708447	SDHAP3	cis	Nerve Tibial	GTEx
rs7708447	SDHAP3	cis	Thyroid	GTEx
rs7708447	SDHAP3	cis	Artery Tibial	GTEx
rs7708447	SDHAP3	cis	Esophagus Mucosa	GTEx
rs7708447	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1565800-1594200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:1566200-1594200	Weak transcription	Brain Substantia Nigra	brain
3	chr5:1568000-1594000	Weak transcription	K562	blood
4	chr5:1568400-1594000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:1568400-1594000	Weak transcription	Right Ventricle	heart
6	chr5:1568800-1594200	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:1568800-1594200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:1569000-1594000	Weak transcription	HSMM	muscle
9	chr5:1569000-1594200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:1569000-1594200	Weak transcription	Psoas Muscle	Psoas
11	chr5:1569400-1594000	Weak transcription	HSMMtube	muscle
12	chr5:1569400-1594000	Weak transcription	HUVEC	blood vessel
13	chr5:1569400-1594200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:1569600-1594000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:1569600-1594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:1569800-1594000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:1570600-1594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:1571200-1594400	Weak transcription	Stomach Mucosa	stomach
19	chr5:1571400-1594000	Weak transcription	A549	lung
20	chr5:1571800-1594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:1571800-1594000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:1571800-1594000	Weak transcription	Small Intestine	intestine
23	chr5:1572600-1594000	Weak transcription	Placenta	Placenta
24	chr5:1573200-1594200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:1578600-1594000	Weak transcription	Esophagus	oesophagus
26	chr5:1579600-1594000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:1579800-1594000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:1582400-1595000	Weak transcription	Fetal Heart	heart
29	chr5:1584400-1594000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:1585200-1593400	Weak transcription	Fetal Thymus	thymus
31	chr5:1585200-1593800	Weak transcription	Fetal Brain Male	brain
32	chr5:1585200-1594000	Weak transcription	Fetal Kidney	kidney
33	chr5:1585200-1594000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:1585400-1594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:1585600-1593600	Strong transcription	Fetal Stomach	stomach
36	chr5:1586000-1593800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:1586400-1594000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:1587200-1592400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:1587400-1592600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:1587400-1593200	Strong transcription	Dnd41	blood
41	chr5:1587400-1593400	Strong transcription	Fetal Intestine Small	intestine
42	chr5:1587600-1592600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:1587800-1592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:1588000-1593400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:1588000-1594000	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:1588200-1594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:1588400-1592800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:1588400-1593600	Weak transcription	Primary B cells from cord blood	blood
49	chr5:1588400-1594000	Weak transcription	Primary T cells from cord blood	blood
50	chr5:1588600-1592400	Strong transcription	H1 Cell Line	embryonic stem cell

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