Variant report

Variant	rs61729488
Chromosome Location	chr3:49067904-49067905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:49067822-49068115	K562	blood:	n/a	n/a
2	TEAD4	chr3:49067796-49068129	K562	blood:	n/a	n/a
3	CEBPD	chr3:49067814-49068170	K562	blood:	n/a	n/a
4	JUND	chr3:49067875-49068040	K562	blood:	n/a	n/a
5	TAL1	chr3:49067795-49068151	K562	blood:	n/a	n/a
6	MAFK	chr3:49067788-49068128	HepG2	liver:	n/a	chr3:49067947-49067962
7	MAFK	chr3:49067843-49068337	K562	blood:	n/a	chr3:49067947-49067962
8	POLR2A	chr3:49067807-49068392	K562	blood:	n/a	n/a
9	EP300	chr3:49067797-49068053	K562	blood:	n/a	n/a
10	POLR2A	chr3:49067776-49068366	Hela-S3	cervix:	n/a	n/a
11	MAFF	chr3:49067800-49068003	K562	blood:	n/a	chr3:49067946-49067964
12	MAFF	chr3:49067826-49068061	HepG2	liver:	n/a	chr3:49067946-49067964
13	POLR2A	chr3:49067880-49068082	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:49067601-49067989	K562	blood:	n/a	n/a
15	POLR2A	chr3:49067765-49068503	K562	blood:	n/a	n/a
16	MAFK	chr3:49067785-49068108	HepG2	liver:	n/a	chr3:49067947-49067962

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48631022..48632850-chr3:49066153..49068061,2	K562	blood:
2	chr3:49062158..49068430-chr3:49139884..49143886,7	K562	blood:
3	chr3:49063558..49068659-chr3:49135988..49142189,8	MCF-7	breast:
4	chr3:49062154..49067981-chr3:49128951..49132856,8	K562	blood:
5	chr3:49065295..49067964-chr3:49130021..49133372,4	MCF-7	breast:
6	chr3:49063985..49068649-chr3:49151287..49155483,4	MCF-7	breast:
7	chr3:49064025..49068089-chr3:49156559..49161197,7	MCF-7	breast:
8	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
9	chr3:49065644..49068081-chr3:49140753..49143557,2	MCF-7	breast:
10	chr3:49067450..49069874-chr3:49105027..49108466,3	K562	blood:
11	chr3:49062784..49068653-chr3:49129538..49133266,11	MCF-7	breast:
12	chr3:49064550..49068051-chr3:49140813..49143886,3	K562	blood:

No data

Variant related genes	Relation type
IMPDH2	TF binding region
ENSG00000114270	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10154895	0.80[EUR][1000 genomes]
rs11552724	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706052	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11712006	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11715689	0.89[AMR][1000 genomes]
rs11715713	0.89[AMR][1000 genomes]
rs11715835	0.85[AMR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11717978	0.84[EUR][1000 genomes]
rs11718982	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13072554	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13080725	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34504524	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34580506	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34889065	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35102816	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35108630	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35283189	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3923475	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56004653	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56306491	1.00[AFR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73084135	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9880088	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs61729488	WDR6	cis	Whole Blood	GTEx
rs61729488	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs61729488	WDR6	cis	Adipose Subcutaneous	GTEx
rs61729488	WDR6	cis	Artery Tibial	GTEx
rs61729488	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs61729488	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49068200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:49066800-49069000	Weak transcription	Ovary	ovary
3	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:49067000-49068000	Weak transcription	Esophagus	oesophagus
6	chr3:49067000-49069000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49067000-49069600	Weak transcription	Aorta	Aorta
8	chr3:49067000-49070000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:49067000-49071200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:49067000-49074200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49067200-49068000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49067200-49068000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:49067200-49068000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:49067200-49068000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:49067200-49068000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:49067200-49068000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:49067200-49068000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:49067200-49068000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:49067200-49068000	Weak transcription	NHLF	lung
20	chr3:49067200-49068200	Weak transcription	Fetal Lung	lung
21	chr3:49067200-49068200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:49067200-49068200	Weak transcription	A549	lung
23	chr3:49067200-49068600	Weak transcription	Fetal Kidney	kidney
24	chr3:49067200-49069000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:49067200-49069000	Weak transcription	HSMM	muscle
26	chr3:49067200-49069600	Genic enhancers	K562	blood
27	chr3:49067200-49069800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:49067200-49070400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:49067200-49072000	Weak transcription	Small Intestine	intestine
30	chr3:49067200-49072200	Weak transcription	Fetal Brain Male	brain
31	chr3:49067200-49074800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:49067200-49078600	Weak transcription	Psoas Muscle	Psoas
33	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
35	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:49067400-49068000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:49067400-49068200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:49067400-49069000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:49067400-49069000	Weak transcription	Fetal Heart	heart
40	chr3:49067400-49069000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:49067400-49069200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:49067400-49069600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:49067400-49069600	Weak transcription	Stomach Mucosa	stomach
44	chr3:49067400-49070000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:49067400-49070000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:49067400-49070000	Strong transcription	HSMMtube	muscle
47	chr3:49067400-49070000	Strong transcription	Osteobl	bone
48	chr3:49067400-49070200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:49067400-49071000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:49067400-49071800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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