Variant report

Variant	rs3782357
Chromosome Location	chr12:49427652-49427653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49427608-49428466	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:49424378-49429068	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:49427413-49427790	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:49427562-49427800	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:49427626-49427998	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:49426997-49427940	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:49426422-49428084	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:49427518-49427871	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:49423730-49429012	K562	blood:	n/a	n/a
10	POLR2A	chr12:49426507-49429294	K562	blood:	n/a	n/a
11	POLR2A	chr12:49424296-49428943	K562	blood:	n/a	n/a
12	POLR2A	chr12:49423727-49428518	HL-60	blood:	n/a	n/a
13	POLR2A	chr12:49427436-49427824	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:49427532-49427873	GM12892	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49378003..49379859-chr12:49427331..49429086,2	K562	blood:
2	chr12:49418592..49421538-chr12:49427562..49429624,2	K562	blood:
3	chr12:49424813..49427751-chr12:49451760..49454466,2	MCF-7	breast:
4	chr12:49411063..49414139-chr12:49425757..49428638,5	MCF-7	breast:
5	chr12:49425028..49428034-chr12:49523264..49526467,3	MCF-7	breast:

No data

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10459221	0.85[ASN][1000 genomes]
rs10459232	0.82[CEU][hapmap];0.85[ASN][1000 genomes]
rs1054442	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10747559	0.89[ASN][1000 genomes]
rs10783299	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783300	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783301	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875906	0.89[ASN][1000 genomes]
rs10875908	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10875911	0.96[ASN][1000 genomes]
rs10875912	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10875913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875914	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875917	0.85[ASN][1000 genomes]
rs10875918	0.84[ASN][1000 genomes]
rs11168822	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168827	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168838	0.87[ASN][1000 genomes]
rs11168839	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168850	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1138908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614738	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12298884	0.82[ASN][1000 genomes]
rs12580349	0.84[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12821008	0.84[ASN][1000 genomes]
rs2117029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241726	0.96[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293445	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293446	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304275	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34436857	0.94[ASN][1000 genomes]
rs3741619	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3741622	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6580698	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6580699	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7296288	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs7300136	0.84[ASN][1000 genomes]
rs7969091	0.81[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs876333	0.99[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3782357	DDN	cis	Muscle Skeletal	GTEx
rs3782357	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs3782357	RP11-386G11.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49413000-49453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49413400-49449000	Strong transcription	Fetal Intestine Small	intestine
3	chr12:49413800-49444000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:49413800-49449200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:49414000-49429600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:49414200-49429200	Strong transcription	Fetal Brain Female	brain
7	chr12:49414200-49449000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:49414400-49429000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:49414400-49429200	Strong transcription	NHLF	lung
10	chr12:49414400-49443000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:49414400-49443600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:49414400-49448800	Strong transcription	Colonic Mucosa	Colon
13	chr12:49414400-49449000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:49414400-49449000	Strong transcription	Brain Cingulate Gyrus	brain
15	chr12:49414400-49449000	Strong transcription	Brain Germinal Matrix	brain
16	chr12:49414400-49449200	Strong transcription	Fetal Stomach	stomach
17	chr12:49414400-49449200	Strong transcription	Fetal Thymus	thymus
18	chr12:49414400-49449200	Strong transcription	Thymus	Thymus
19	chr12:49414400-49449400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:49414400-49449400	Strong transcription	Fetal Intestine Large	intestine
21	chr12:49414400-49449800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:49414600-49427800	Strong transcription	Brain Anterior Caudate	brain
23	chr12:49414600-49428800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:49414600-49429400	Strong transcription	Lung	lung
25	chr12:49414600-49429400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr12:49414600-49429400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:49414600-49433000	Strong transcription	Placenta	Placenta
28	chr12:49414600-49439600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:49414600-49442600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:49414600-49443200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:49414600-49443200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr12:49414600-49448600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:49414600-49448600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:49414600-49448600	Strong transcription	Adipose Nuclei	Adipose
35	chr12:49414600-49448800	Strong transcription	Ovary	ovary
36	chr12:49414600-49449000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:49414600-49449000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:49414600-49449000	Strong transcription	Primary T cells from cord blood	blood
39	chr12:49414600-49449400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:49414600-49449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:49414600-49449800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49414800-49429200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:49414800-49429400	Strong transcription	Left Ventricle	heart
44	chr12:49414800-49435400	Strong transcription	A549	lung
45	chr12:49414800-49447200	Strong transcription	Dnd41	blood
46	chr12:49414800-49448200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:49414800-49449200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:49414800-49449200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:49414800-49449400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:49414800-49449400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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