Variant report

Variant	rs10747783
Chromosome Location	chr12:58176614-58176615
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	RAD21	chr12:58176247-58176667	SK-N-SH_RA	brain:	n/a	chr12:58176461-58176480 chr12:58176550-58176564 chr12:58176462-58176476 chr12:58176460-58176474 chr12:58176462-58176471 chr12:58176464-58176477
2	MYC	chr12:58176190-58176936	K562	blood:	n/a	n/a
3	POLR2A	chr12:58176290-58176895	GM12878	blood:	n/a	n/a
4	TAF1	chr12:58176250-58176963	ECC-1	luminal epithelium:	n/a	n/a
5	MYC	chr12:58176350-58176741	HUVEC	blood vessel:	n/a	n/a
6	RAD21	chr12:58176220-58176738	H1-hESC	embryonic stem cell:	n/a	chr12:58176461-58176480 chr12:58176550-58176564 chr12:58176462-58176476 chr12:58176460-58176474 chr12:58176462-58176471 chr12:58176464-58176477
7	EGR1	chr12:58176349-58176615	GM12878	blood:	n/a	n/a
8	SP2	chr12:58176296-58176729	H1-hESC	embryonic stem cell:	n/a	n/a
9	ETS1	chr12:58176378-58176749	K562	blood:	n/a	n/a
10	ZBTB33	chr12:58176217-58176779	HCT-116	colon:	n/a	n/a
11	MXI1	chr12:58176322-58176757	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:58176328-58176665	GM12892	blood:	n/a	chr12:58176463-58176476 chr12:58176460-58176478 chr12:58176461-58176477 chr12:58176463-58176471 chr12:58176550-58176563 chr12:58176462-58176483
13	JUND	chr12:58176317-58176737	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr12:58176334-58176701	Fibrobl	skin:	n/a	chr12:58176463-58176476 chr12:58176460-58176478 chr12:58176461-58176477 chr12:58176463-58176471 chr12:58176550-58176563 chr12:58176462-58176483
15	ZBTB33	chr12:58176246-58176725	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:58176273-58176974	HCT-116	colon:	n/a	n/a
17	POLR2A	chr12:58176246-58176869	K562	blood:	n/a	n/a
18	TAF1	chr12:58176372-58176787	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:58176302-58177144	Hela-S3	cervix:	n/a	n/a
20	MYC	chr12:58176394-58176833	K562	blood:	n/a	n/a
21	SIN3A	chr12:58176370-58176982	GM12878	blood:	n/a	chr12:58176651-58176660
22	REST	chr12:58176405-58176617	HepG2	liver:	n/a	n/a
23	TCF12	chr12:58176058-58177014	ECC-1	luminal epithelium:	n/a	n/a
24	ATF3	chr12:58176197-58176932	A549	lung:	n/a	chr12:58176519-58176528
25	YY1	chr12:58176265-58176740	SK-N-SH_RA	brain:	n/a	n/a
26	HCFC1	chr12:58176185-58176800	K562	blood:	n/a	n/a
27	PAX5	chr12:58176305-58176709	GM12878	blood:	n/a	n/a
28	CEBPB	chr12:58176265-58176883	MCF-7	breast:	n/a	n/a
29	CEBPB	chr12:58176299-58176809	K562	blood:	n/a	n/a
30	SRF	chr12:58176393-58176670	K562	blood:	n/a	n/a
31	EP300	chr12:58176294-58177010	K562	blood:	n/a	n/a
32	MYC	chr12:58176364-58176902	MCF-7	breast:	n/a	n/a
33	TCF7L2	chr12:58176344-58176646	PANC-1	pancreas:	n/a	n/a
34	CTCF	chr12:58176332-58176653	GM12891	blood:	n/a	chr12:58176463-58176476 chr12:58176460-58176478 chr12:58176461-58176477 chr12:58176463-58176471 chr12:58176550-58176563 chr12:58176462-58176483
35	ETS1	chr12:58176275-58176827	A549	lung:	n/a	n/a
36	YY1	chr12:58176339-58176780	GM12891	blood:	n/a	n/a
37	CHD2	chr12:58176396-58176843	HepG2	liver:	n/a	n/a
38	RXRA	chr12:58176203-58176680	GM12878	blood:	n/a	chr12:58176460-58176480
39	ETS1	chr12:58176348-58177109	K562	blood:	n/a	n/a
40	MXI1	chr12:58176347-58176959	K562	blood:	n/a	n/a
41	REST	chr12:58176281-58176839	HepG2	liver:	n/a	chr12:58176381-58176394
42	POLR2A	chr12:58176231-58177044	NB4	blood:	n/a	n/a
43	BCLAF1	chr12:58176273-58177042	GM12878	blood:	n/a	chr12:58176518-58176527
44	ELF1	chr12:58176211-58176776	GM12878	blood:	n/a	n/a
45	CTCF	chr12:58176307-58176661	SK-N-SH_RA	brain:	n/a	chr12:58176463-58176476 chr12:58176460-58176478 chr12:58176461-58176477 chr12:58176463-58176471 chr12:58176550-58176563 chr12:58176462-58176483
46	YY1	chr12:58176342-58176727	K562	blood:	n/a	n/a
47	POLR2A	chr12:58176291-58176874	GM12891	blood:	n/a	n/a
48	UBTF	chr12:58176383-58176770	K562	blood:	n/a	n/a
49	CTCF	chr12:58176311-58176711	Spleen_OC	spleen:	n/a	chr12:58176463-58176476 chr12:58176460-58176478 chr12:58176461-58176477 chr12:58176463-58176471 chr12:58176550-58176563 chr12:58176462-58176483
50	POLR2A	chr12:58176199-58176979	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58086909..58089805-chr12:58175888..58177930,2	K562	blood:
2	chr12:58165740..58166574-chr12:58176461..58177013,2	Hela-S3	cervix:
3	chr12:58175489..58177867-chr12:58239241..58240765,2	MCF-7	breast:
4	chr12:58174276..58176764-chr12:58197954..58200651,2	K562	blood:
5	chr12:58176542..58178155-chr12:58239377..58241593,2	K562	blood:
6	chr12:58176052..58177919-chr12:58192741..58195580,2	MCF-7	breast:
7	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
8	chr12:58146595..58149356-chr12:58175469..58178051,2	K562	blood:
9	chr12:58175049..58178042-chr12:58240093..58242141,3	K562	blood:

Variant related genes	Relation type
TSFM	TF binding region
ENSG00000166896	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000206749	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1021469	0.91[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10431505	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877011	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10877012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877017	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172342	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172350	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.84[JPT][hapmap]
rs1599931	0.88[JPT][hapmap]
rs1599932	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875125	0.89[JPT][hapmap]
rs2014886	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069506	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782130	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap]
rs4646536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap]
rs4760339	0.83[JPT][hapmap]
rs4760341	0.83[JPT][hapmap]
rs56177740	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs703842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9652011	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs10747783	METTL21B	cis	lung	GTEx
rs10747783	CYP27B1	cis	Thyroid	GTEx
rs10747783	FAM119B	cis	Lymphoblastoid	GTEx
rs10747783	METTL21B	cis	Muscle Skeletal	GTEx
rs10747783	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs10747783	TSFM	cis	Muscle Skeletal	GTEx
rs10747783	FAM119B	cis	Brain Pons	GTEx
rs10747783	METTL21B	cis	Esophagus Mucosa	GTEx
rs10747783	XRCC6BP1	cis	Whole Blood	GTEx
rs10747783	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10747783	TSFM	cis	multi-tissue	Pritchard
rs10747783	METTL21B	cis	Whole Blood	GTEx
rs10747783	METTL21B	cis	Heart Left Ventricle	GTEx
rs10747783	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10747783	RP11-571M6.13	cis	Thyroid	GTEx
rs10747783	METTL21B	cis	Esophagus Muscularis	GTEx
rs10747783	DKFZP586D0919	cis	multi-tissue	Pritchard
rs10747783	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10747783	FAM119B	cis	Cerebellum	GTEx
rs10747783	FAM119B	cis	Frontal Cortex	GTEx
rs10747783	METTL21B	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58176000-58177200	Active TSS	Fetal Lung	lung
2	chr12:58176000-58177400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:58176000-58177400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:58176200-58176800	Active TSS	Brain Angular Gyrus	brain
5	chr12:58176200-58176800	Active TSS	Fetal Muscle Trunk	muscle
6	chr12:58176200-58176800	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr12:58176200-58177000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:58176200-58177000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:58176200-58177000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:58176200-58177000	Active TSS	Brain Anterior Caudate	brain
11	chr12:58176200-58177000	Active TSS	Brain Hippocampus Middle	brain
12	chr12:58176200-58177000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:58176200-58177000	Active TSS	Brain Substantia Nigra	brain
14	chr12:58176200-58177000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr12:58176200-58177000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr12:58176200-58177000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:58176200-58177200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:58176200-58177200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr12:58176200-58177200	Active TSS	Stomach Smooth Muscle	stomach
20	chr12:58176200-58177400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:58176200-58177400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr12:58176200-58177400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:58176200-58177400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:58176200-58177400	Active TSS	Psoas Muscle	Psoas
25	chr12:58176200-58177400	Active TSS	Right Atrium	heart
26	chr12:58176200-58177400	Active TSS	NHDF-Ad	bronchial
27	chr12:58176200-58177600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:58176200-58177600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:58176200-58177800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:58176400-58176800	Active TSS	Primary B cells from cord blood	blood
31	chr12:58176400-58176800	Active TSS	Primary B cells from peripheral blood	blood
32	chr12:58176400-58176800	Active TSS	Primary T cells fromperipheralblood	blood
33	chr12:58176400-58176800	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr12:58176400-58176800	Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr12:58176400-58176800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr12:58176400-58176800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:58176400-58176800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:58176400-58176800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:58176400-58176800	Active TSS	Adipose Nuclei	Adipose
40	chr12:58176400-58176800	Active TSS	Liver	Liver
41	chr12:58176400-58176800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr12:58176400-58176800	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:58176400-58176800	Active TSS	Right Ventricle	heart
44	chr12:58176400-58176800	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr12:58176400-58177000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:58176400-58177000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:58176400-58177000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:58176400-58177000	Active TSS	Primary T cells from cord blood	blood
49	chr12:58176400-58177000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:58176400-58177000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links