Variant report

Variant	rs12202025
Chromosome Location	chr6:79945057-79945058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:79943222-79945113	HEK293	kidney:	n/a	chr6:79943761-79943769
2	EP300	chr6:79944918-79945118	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:79942900-79945349	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr6:79942075-79945226	SK-N-SH	brain:	n/a	chr6:79944581-79944596
5	KAP1	chr6:79942796-79945275	U2OS	brain:	n/a	chr6:79943761-79943769

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
3	chr6:79787878..79790499-chr6:79943656..79946271,3	K562	blood:
4	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK1BP1-1	chr6:79943779-79946510	ENSG00000247783
2	lnc-IRAK1BP1-1	chr6:79943779-79946517	NONHSAT113679
3	lnc-IRAK1BP1-1	chr6:79944457-79946310	NONHSAT113680
4	lnc-IRAK1BP1-1	chr6:79943779-79946514	ENSG00000270362.1

No data

Variant related genes	Relation type
HMGN3	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10455357	0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12207187	0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12202025	IMPG1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79944400-79948400	Weak transcription	Left Ventricle	heart
2	chr6:79944400-79948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:79944400-79948600	Weak transcription	Stomach Mucosa	stomach
4	chr6:79944400-79948800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:79944400-79950400	Weak transcription	Lung	lung
6	chr6:79944600-79948600	Weak transcription	Ovary	ovary
7	chr6:79944600-79948600	Weak transcription	Pancreas	Pancrea
8	chr6:79944600-79948600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:79944800-79945200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:79944800-79945200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:79944800-79946200	Weak transcription	Thymus	Thymus
12	chr6:79944800-79946200	Weak transcription	NHDF-Ad	bronchial
13	chr6:79944800-79947400	Weak transcription	NH-A	brain
14	chr6:79944800-79947600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:79944800-79947600	Weak transcription	GM12878-XiMat	blood
16	chr6:79944800-79948600	Weak transcription	Liver	Liver
17	chr6:79944800-79948600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:79944800-79948600	Weak transcription	Fetal Intestine Small	intestine
19	chr6:79944800-79948600	Weak transcription	Right Atrium	heart
20	chr6:79944800-79948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:79944800-79948600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:79944800-79948600	Weak transcription	NHEK	skin
23	chr6:79944800-79948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:79944800-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:79944800-79948800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:79944800-79949200	Weak transcription	HMEC	breast
27	chr6:79944800-79950400	Weak transcription	Right Ventricle	heart
28	chr6:79945000-79945600	Enhancers	Dnd41	blood
29	chr6:79945000-79946200	Weak transcription	Fetal Thymus	thymus
30	chr6:79945000-79947800	Weak transcription	Hela-S3	cervix
31	chr6:79945000-79948400	Weak transcription	Fetal Heart	heart
32	chr6:79945000-79948400	Weak transcription	HepG2	liver
33	chr6:79945000-79948600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:79945000-79948600	Weak transcription	Placenta	Placenta
35	chr6:79945000-79948800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:79945000-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:79945000-79949000	Weak transcription	Psoas Muscle	Psoas
38	chr6:79945000-79955400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links