Variant report

Variant	rs1134043
Chromosome Location	chr3:49200137-49200138
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49200058-49200915	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:49198751-49201892	HL-60	blood:	n/a	n/a
3	POLR2A	chr3:49198739-49201514	K562	blood:	n/a	n/a
4	POLR2A	chr3:49198510-49204140	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:49200038-49200879	HCT-116	colon:	n/a	n/a
6	POLR2A	chr3:49200072-49200925	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:49200128-49200335	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:49200093-49201882	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:49200061-49201936	K562	blood:	n/a	n/a
10	POLR2A	chr3:49200061-49200393	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:49200072-49201232	HCT-116	colon:	n/a	n/a
12	POLR2A	chr3:49199971-49200222	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:49200054-49200910	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49198535-49201959	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:49200065-49200934	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:49200090-49201015	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr3:49200068-49200832	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr3:49200066-49201010	GM12891	blood:	n/a	n/a
19	USF2	chr3:49200132-49201205	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:49197955-49203552	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr3:49200066-49200927	K562	blood:	n/a	n/a
22	POLR2A	chr3:49200089-49200830	HL-60	blood:	n/a	n/a
23	POLR2A	chr3:49199225-49200865	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:49200115-49200414	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:49200095-49200827	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:49200123-49200770	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:49200065-49202013	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:49198739-49201658	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:49200032-49200854	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:49198512-49204161	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:49198105-49200990	K562	blood:	n/a	n/a
32	POLR2A	chr3:49200073-49200369	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:49200063-49200584	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49192110..49194166-chr3:49199747..49201408,2	MCF-7	breast:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49168509..49171088-chr3:49198215..49200498,3	K562	blood:
4	chr3:49067951..49070552-chr3:49199245..49201626,2	K562	blood:
5	chr3:49166454..49167956-chr3:49197730..49200400,2	K562	blood:
6	chr3:49027656..49029383-chr3:49199961..49201942,2	MCF-7	breast:
7	chr3:49198168..49200645-chr3:49211215..49212732,2	K562	blood:
8	chr3:49057940..49060006-chr3:49197956..49200673,2	MCF-7	breast:
9	chr3:49055738..49057542-chr3:49200066..49202706,2	K562	blood:
10	chr3:49199767..49200734-chr5:43040560..43041196,2	Hela-S3	cervix:
11	chr3:49199406..49201947-chr3:49447942..49450781,2	MCF-7	breast:
12	chr3:49170619..49172882-chr3:49199915..49201887,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270441	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10049462	0.93[CEU][hapmap]
rs10865954	0.96[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs11552724	0.92[CEU][hapmap]
rs11706052	0.93[CEU][hapmap]
rs11706189	0.92[CEU][hapmap]
rs11713297	0.93[CEU][hapmap]
rs11715581	0.85[LWK][hapmap];0.80[YRI][hapmap]
rs11716614	0.85[CEU][hapmap]
rs11719220	0.93[CEU][hapmap]
rs13068038	0.93[CEU][hapmap]
rs13077498	0.93[CEU][hapmap]
rs13086240	0.93[CEU][hapmap]
rs34566463	0.93[CEU][hapmap]
rs34580506	0.93[CEU][hapmap]
rs35060561	0.93[CEU][hapmap]
rs35283189	0.93[CEU][hapmap]
rs35673421	0.93[CEU][hapmap]
rs36133651	0.81[AFR][1000 genomes]
rs4308307	0.87[AFR][1000 genomes]
rs4513485	0.89[LWK][hapmap];0.96[YRI][hapmap]
rs4955410	0.89[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs4955419	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4955420	0.91[LWK][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs5030795	0.93[CEU][hapmap]
rs9311439	0.90[CEU][hapmap]
rs9814987	0.93[CEU][hapmap]
rs9837237	0.93[CEU][hapmap]
rs9837625	0.93[CEU][hapmap]
rs9844757	0.93[CEU][hapmap]
rs9847839	0.93[CEU][hapmap]
rs9880088	0.93[CEU][hapmap]
rs9880309	0.91[CEU][hapmap]
rs9990153	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1134043	COL7A1	cis	parietal	SCAN
rs1134043	CSPG5	cis	parietal	SCAN
rs1134043	WDR6	cis	lung	GTEx
rs1134043	CCDC71	cis	cerebellum	SCAN
rs1134043	C3orf62	cis	cerebellum	SCAN
rs1134043	ARIH2	cis	cerebellum	SCAN
rs1134043	WDR6	cis	parietal	SCAN
rs1134043	WDR6	cis	Whole Blood	GTEx
rs1134043	WDR6	cis	lymphoblastoid	seeQTL
rs1134043	LRRC2	cis	cerebellum	SCAN
rs1134043	WDR6	cis	Adipose Subcutaneous	GTEx
rs1134043	QRICH1	cis	cerebellum	SCAN
rs1134043	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs1134043	WDR6	cis	Esophagus Mucosa	GTEx
rs1134043	BSN	cis	cerebellum	SCAN
rs1134043	NISCH	cis	cerebellum	SCAN
rs1134043	WDR6	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
3	chr3:49195200-49200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:49195200-49202400	Weak transcription	Fetal Kidney	kidney
5	chr3:49195400-49200400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:49195600-49200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:49195600-49200200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:49195600-49200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:49195600-49200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:49195600-49200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:49195600-49200400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:49195600-49202200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:49196000-49202400	Strong transcription	Fetal Stomach	stomach
14	chr3:49196200-49200200	Weak transcription	Fetal Lung	lung
15	chr3:49196400-49200400	Weak transcription	HepG2	liver
16	chr3:49196400-49202200	Weak transcription	Right Atrium	heart
17	chr3:49196600-49200400	Weak transcription	HSMMtube	muscle
18	chr3:49196600-49200600	Weak transcription	NHDF-Ad	bronchial
19	chr3:49196600-49200800	Weak transcription	Hela-S3	cervix
20	chr3:49196800-49200200	Weak transcription	Left Ventricle	heart
21	chr3:49196800-49200200	Weak transcription	HMEC	breast
22	chr3:49197200-49200200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:49197200-49200200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:49197400-49201000	Weak transcription	K562	blood
25	chr3:49197600-49200200	Weak transcription	Liver	Liver
26	chr3:49197600-49200400	Weak transcription	Colonic Mucosa	Colon
27	chr3:49197800-49200200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49197800-49200400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:49197800-49200400	Weak transcription	Osteobl	bone
30	chr3:49198000-49200400	Weak transcription	HUVEC	blood vessel
31	chr3:49198000-49201800	Strong transcription	Thymus	Thymus
32	chr3:49198000-49202200	Weak transcription	Small Intestine	intestine
33	chr3:49198000-49202400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:49198200-49200400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:49198200-49201600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:49198200-49201600	Strong transcription	Aorta	Aorta
37	chr3:49198200-49201600	Strong transcription	Brain Germinal Matrix	brain
38	chr3:49198200-49202000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:49198200-49202000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:49198200-49202200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:49198200-49202200	Strong transcription	Fetal Brain Female	brain
42	chr3:49198200-49202400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr3:49198600-49200200	Weak transcription	A549	lung
44	chr3:49198600-49201800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49198600-49201800	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:49198600-49202000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:49198800-49200200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr3:49198800-49200400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49198800-49200400	Strong transcription	Ovary	ovary
50	chr3:49198800-49200600	Strong transcription	Dnd41	blood

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