Variant report

Variant	rs3782235
Chromosome Location	chr12:56915547-56915548
allele	A/G
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	MAZ	chr12:56915105-56916974	IMR90	lung:	n/a	n/a
2	ATF1	chr12:56915417-56915712	K562	blood:	n/a	n/a
3	FOXA1	chr12:56915350-56915699	HepG2	liver:	n/a	chr12:56915506-56915518
4	FOXA1	chr12:56915375-56915632	HepG2	liver:	n/a	chr12:56915506-56915518
5	POLR2A	chr12:56915361-56915827	HUVEC	blood vessel:	n/a	n/a
6	STAT1	chr12:56915529-56915589	GM12878	blood:	n/a	n/a
7	CREB1	chr12:56915431-56915716	A549	lung:	n/a	n/a
8	MYC	chr12:56915519-56915728	MCF10A-Er-Src	breast:	n/a	n/a
9	SP1	chr12:56915198-56916345	HCT-116	colon:	n/a	chr12:56916221-56916231 chr12:56915336-56915343
10	CREB1	chr12:56915352-56915681	HepG2	liver:	n/a	n/a
11	FOSL1	chr12:56915147-56915894	HCT-116	colon:	n/a	n/a
12	TBL1XR1	chr12:56915388-56915654	K562	blood:	n/a	n/a
13	CREB1	chr12:56915383-56915798	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXA2	chr12:56915316-56915857	A549	lung:	n/a	chr12:56915506-56915518
15	POLR2A	chr12:56915517-56916225	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF143	chr12:56915351-56915753	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr12:56915256-56915928	ECC-1	luminal epithelium:	n/a	n/a
18	ATF2	chr12:56915331-56915709	H1-hESC	embryonic stem cell:	n/a	chr12:56915588-56915599
19	POLR2A	chr12:56915482-56915561	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:56915302-56916107	SK-N-MC	brain:	n/a	n/a
21	FOSL1	chr12:56915320-56915697	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZNF384	chr12:56915077-56915693	K562	blood:	n/a	n/a
23	MAZ	chr12:56915495-56915760	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:56915331-56915929	SK-N-MC	brain:	n/a	n/a
25	FOSL1	chr12:56915404-56915718	K562	blood:	n/a	n/a
26	ATF2	chr12:56915396-56915698	GM12878	blood:	n/a	chr12:56915588-56915599
27	CREB1	chr12:56915465-56915772	A549	lung:	n/a	n/a
28	RCOR1	chr12:56915121-56915635	K562	blood:	n/a	n/a
29	FOS	chr12:56915436-56915596	MCF10A-Er-Src	breast:	n/a	n/a
30	MAX	chr12:56915493-56915754	Hela-S3	cervix:	n/a	n/a
31	TEAD4	chr12:56915407-56915809	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr12:56915360-56915865	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr12:56915476-56915707	H1-hESC	embryonic stem cell:	n/a	chr12:56915622-56915633
34	MAX	chr12:56915253-56915733	A549	lung:	n/a	n/a
35	POLR2A	chr12:56915384-56916817	HUVEC	blood vessel:	n/a	n/a
36	MAFK	chr12:56915436-56915588	K562	blood:	n/a	n/a
37	SIN3AK20	chr12:56915382-56916294	A549	lung:	n/a	n/a
38	SP1	chr12:56915222-56915927	HCT-116	colon:	n/a	chr12:56915336-56915343
39	STAT3	chr12:56915164-56915614	MCF10A-Er-Src	breast:	n/a	chr12:56915382-56915389
40	POLR2A	chr12:56915397-56915946	SK-N-SH	brain:	n/a	n/a
41	MAZ	chr12:56915431-56915875	K562	blood:	n/a	n/a
42	CBX3	chr12:56915286-56916838	HCT-116	colon:	n/a	n/a
43	FOSL1	chr12:56915409-56915697	H1-hESC	embryonic stem cell:	n/a	n/a
44	SP1	chr12:56915263-56916957	A549	lung:	n/a	chr12:56916221-56916231 chr12:56915336-56915343
45	ATF2	chr12:56915360-56915722	GM12878	blood:	n/a	chr12:56915588-56915599
46	MAZ	chr12:56915510-56915763	GM12878	blood:	n/a	n/a
47	ATF2	chr12:56915333-56915862	H1-hESC	embryonic stem cell:	n/a	chr12:56915588-56915599
48	POLR2A	chr12:56915468-56915936	Hela-S3	cervix:	n/a	n/a
49	ATF3	chr12:56915300-56915723	A549	lung:	n/a	chr12:56915589-56915597 chr12:56915587-56915597
50	FOXA1	chr12:56915441-56915615	ECC-1	luminal epithelium:	n/a	chr12:56915506-56915518

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56913236..56916197-chr12:57081511..57083245,2	K562	blood:

Variant related genes	Relation type
RBMS2	TF binding region
ENSG00000110958	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10735863	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783786	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876891	0.81[CEU][hapmap];0.96[MEX][hapmap]
rs10876897	0.91[ASN][1000 genomes]
rs10876899	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876902	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876903	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11171883	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11171884	0.80[EUR][1000 genomes]
rs11171887	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11614642	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12814413	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965307	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638285	0.93[LWK][hapmap]
rs2638334	0.93[LWK][hapmap]
rs2638335	0.92[LWK][hapmap]
rs34900037	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34948728	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4759247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581097	0.84[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581098	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6581099	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7131699	0.80[JPT][hapmap]
rs7132918	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7132965	0.89[EUR][1000 genomes]
rs7136456	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7299115	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7303549	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7303717	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7305759	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7313637	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313983	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7314300	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7975238	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3782235	AMHR2	cis	cerebellum	SCAN
rs3782235	RBMS2	cis	Esophagus Mucosa	GTEx
rs3782235	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs3782235	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs3782235	RBMS2	cis	lymphoblastoid	seeQTL
rs3782235	SNORD59A	cis	cerebellum	SCAN
rs3782235	RBMS2	cis	multi-tissue	Pritchard
rs3782235	RBMS2	cis	Whole Blood	GTEx
rs3782235	ITGA5	cis	cerebellum	SCAN
rs3782235	OR6C76	cis	parietal	SCAN
rs3782235	ATF7	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56912200-56915800	Weak transcription	Gastric	stomach
2	chr12:56912200-56915800	Weak transcription	Lung	lung
3	chr12:56912800-56915600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:56912800-56917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:56914000-56915800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:56914000-56916600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:56914000-56917000	Active TSS	Aorta	Aorta
8	chr12:56914000-56917400	Active TSS	Right Atrium	heart
9	chr12:56914000-56917400	Active TSS	Right Ventricle	heart
10	chr12:56914000-56918400	Active TSS	Stomach Smooth Muscle	stomach
11	chr12:56914000-56919200	Weak transcription	Spleen	Spleen
12	chr12:56914200-56916200	Active TSS	Brain Hippocampus Middle	brain
13	chr12:56914200-56916200	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr12:56914200-56916800	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:56914200-56917200	Active TSS	Psoas Muscle	Psoas
16	chr12:56914400-56915600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:56914400-56915800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:56914400-56915800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:56914400-56918600	Active TSS	NHLF	lung
20	chr12:56914600-56915600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr12:56914600-56915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:56914600-56916200	Active TSS	Brain Angular Gyrus	brain
23	chr12:56914600-56916400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:56914600-56916600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr12:56914800-56915600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:56914800-56916000	Active TSS	Brain Substantia Nigra	brain
27	chr12:56914800-56916600	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:56915000-56915600	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr12:56915000-56916000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:56915000-56916200	Active TSS	Small Intestine	intestine
31	chr12:56915000-56916400	Active TSS	Pancreas	Pancrea
32	chr12:56915000-56916400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr12:56915000-56917000	Active TSS	Ovary	ovary
34	chr12:56915000-56917200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:56915000-56917200	Active TSS	Colonic Mucosa	Colon
36	chr12:56915000-56917200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:56915000-56917600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:56915000-56917600	Active TSS	NHDF-Ad	bronchial
39	chr12:56915000-56918600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:56915000-56918600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr12:56915200-56915600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr12:56915200-56915600	Flanking Active TSS	Fetal Heart	heart
43	chr12:56915200-56915600	Flanking Active TSS	NH-A	brain
44	chr12:56915200-56915800	Active TSS	Fetal Thymus	thymus
45	chr12:56915200-56916000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr12:56915200-56916000	Active TSS	Adipose Nuclei	Adipose
47	chr12:56915200-56916000	Active TSS	Brain Germinal Matrix	brain
48	chr12:56915200-56916000	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:56915200-56916200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56915200-56916200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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