Variant report

Variant	rs10785661
Chromosome Location	chr12:47579097-47579098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:47578403-47579143	MCF-7	breast:	n/a	n/a
2	JUND	chr12:47578927-47579128	HepG2	liver:	n/a	n/a
3	SRF	chr12:47578679-47579205	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr12:47577981-47579162	ECC-1	luminal epithelium:	n/a	n/a
5	MYC	chr12:47578605-47579103	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr12:47578572-47579203	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:47474476..47477081-chr12:47578294..47580063,2	MCF-7	breast:
2	chr12:47571772..47573716-chr12:47578864..47580803,2	MCF-7	breast:
3	chr12:47569457..47573425-chr12:47575157..47580264,4	MCF-7	breast:
4	chr12:47482017..47484869-chr12:47577202..47579139,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4698	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10785660	0.86[EUR][1000 genomes]
rs10881056	0.83[EUR][1000 genomes]
rs10881057	0.82[EUR][1000 genomes]
rs10881058	0.86[EUR][1000 genomes]
rs10881064	0.80[CEU][hapmap]
rs11183769	0.85[EUR][1000 genomes]
rs11183774	0.83[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs12371765	0.82[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs12578995	0.83[CEU][hapmap];0.85[CHB][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1357933	0.85[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1357935	0.80[TSI][hapmap]
rs1525453	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1830054	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1880600	0.87[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768777	0.83[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6582696	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7295263	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7299627	0.86[EUR][1000 genomes]
rs7311824	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.87[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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS 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	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv976743	chr12:47573169-47582750	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10785661	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47550600-47582400	Weak transcription	Aorta	Aorta
2	chr12:47551200-47583600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:47554800-47579600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:47557800-47581600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:47558600-47580200	Weak transcription	Primary B cells from cord blood	blood
6	chr12:47558800-47582200	Weak transcription	NH-A	brain
7	chr12:47558800-47582400	Weak transcription	Lung	lung
8	chr12:47559000-47582200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:47566600-47582400	Weak transcription	HSMM	muscle
10	chr12:47568200-47580800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:47570600-47582800	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:47570800-47580200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:47571200-47581600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:47573200-47580400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:47574200-47582400	Weak transcription	Spleen	Spleen
16	chr12:47576000-47582400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:47576200-47582200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr12:47576600-47580000	Weak transcription	K562	blood
19	chr12:47576600-47580400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:47576800-47581000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:47577800-47579400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr12:47577800-47579400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:47578000-47579400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:47578000-47579400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:47578000-47579600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:47578000-47579600	Enhancers	NHEK	skin
27	chr12:47578000-47579800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:47578000-47579800	Enhancers	HMEC	breast
29	chr12:47578000-47582400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:47578200-47579600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:47578200-47587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:47578400-47583800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:47578600-47579400	Enhancers	A549	lung
34	chr12:47578800-47579200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:47578800-47579200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:47578800-47579200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr12:47578800-47579200	Enhancers	Liver	Liver
38	chr12:47578800-47579400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:47578800-47579400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:47578800-47579400	Enhancers	Pancreas	Pancrea
41	chr12:47579000-47579200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links