Variant report

Variant	rs790017
Chromosome Location	chr12:64611986-64611987
allele	C/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	IRF1	chr12:64611974-64614146	K562	blood:	n/a	chr12:64613168-64613182 chr12:64612612-64612626 chr12:64612616-64612627 chr12:64612792-64612802 chr12:64612613-64612626 chr12:64612609-64612630 chr12:64612614-64612626

No.	Distal block	Cell Line	Cell type
1	chr12:64605413..64608740-chr12:64610311..64612005,3	K562	blood:
2	chr12:64597294..64599096-chr12:64610532..64612445,2	MCF-7	breast:
3	chr12:64609478..64611055-chr12:64611155..64613001,2	K562	blood:
4	chr12:64611943..64613525-chr12:64614250..64616027,2	K562	blood:

Variant related genes	Relation type
RPS11P6	TF binding region
ENSG00000212298	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10459258	1.00[AMR][1000 genomes]
rs10459259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10735920	1.00[AMR][1000 genomes]
rs10735921	1.00[AMR][1000 genomes]
rs10735922	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10878133	1.00[AMR][1000 genomes]
rs10878145	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1162970	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11830260	1.00[AMR][1000 genomes]
rs11835078	1.00[AMR][1000 genomes]
rs1436361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1469862	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1657051	1.00[AMR][1000 genomes]
rs1708200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1865796	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1898221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2082951	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2335390	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2453509	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2575290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2575294	1.00[AMR][1000 genomes]
rs35744300	1.00[AMR][1000 genomes]
rs4237925	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4522269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4572232	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4763015	0.96[AFR][1000 genomes]
rs4763153	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4763155	0.81[AFR][1000 genomes]
rs4763156	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6421211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581542	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs696658	1.00[AMR][1000 genomes]
rs696659	1.00[AMR][1000 genomes]
rs699629	1.00[AMR][1000 genomes]
rs699630	1.00[AMR][1000 genomes]
rs699631	1.00[AMR][1000 genomes]
rs699632	1.00[AMR][1000 genomes]
rs699635	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs699636	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs699637	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs699638	1.00[AMR][1000 genomes]
rs7488560	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs789723	1.00[AMR][1000 genomes]
rs789726	1.00[AMR][1000 genomes]
rs789727	1.00[AMR][1000 genomes]
rs789728	1.00[AMR][1000 genomes]
rs789730	1.00[AMR][1000 genomes]
rs789738	1.00[AMR][1000 genomes]
rs789742	1.00[AMR][1000 genomes]
rs789747	1.00[AMR][1000 genomes]
rs790013	1.00[AMR][1000 genomes]
rs790014	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7955105	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7976524	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs809322	1.00[AMR][1000 genomes]
rs813156	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64575000-64615200	Weak transcription	Psoas Muscle	Psoas
2	chr12:64575600-64615000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:64575800-64615200	Weak transcription	Fetal Stomach	stomach
4	chr12:64576000-64615000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:64581400-64614600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:64581800-64615400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:64582600-64614600	Weak transcription	Hela-S3	cervix
8	chr12:64582600-64614600	Weak transcription	NHDF-Ad	bronchial
9	chr12:64583200-64615400	Weak transcription	Placenta	Placenta
10	chr12:64584800-64615200	Weak transcription	Thymus	Thymus
11	chr12:64586200-64615200	Weak transcription	Right Ventricle	heart
12	chr12:64588200-64613000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:64588400-64613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:64588400-64613000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:64588400-64614000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:64588400-64614600	Weak transcription	HMEC	breast
17	chr12:64588400-64614800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:64588400-64615000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:64588400-64615000	Weak transcription	HSMM	muscle
20	chr12:64588400-64615200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:64588400-64615400	Weak transcription	Spleen	Spleen
22	chr12:64588600-64612400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:64589000-64613000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:64589000-64613800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:64589000-64614800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:64589000-64614800	Weak transcription	Fetal Thymus	thymus
27	chr12:64589000-64615200	Weak transcription	Fetal Intestine Large	intestine
28	chr12:64589000-64615600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:64589400-64612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:64589400-64614600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:64589600-64612000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:64589800-64612400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:64594600-64615000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:64595200-64613000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:64597400-64615200	Weak transcription	HSMMtube	muscle
36	chr12:64597400-64615400	Weak transcription	Left Ventricle	heart
37	chr12:64598000-64613200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:64598000-64614000	Weak transcription	Brain Angular Gyrus	brain
39	chr12:64598000-64614000	Weak transcription	Brain Substantia Nigra	brain
40	chr12:64598000-64615400	Weak transcription	Aorta	Aorta
41	chr12:64598200-64612400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:64598600-64613800	Weak transcription	Pancreas	Pancrea
43	chr12:64598600-64615000	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:64600200-64615200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:64601600-64615400	Weak transcription	Lung	lung
46	chr12:64601800-64614000	Weak transcription	HepG2	liver
47	chr12:64602000-64614600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:64602400-64614800	Weak transcription	Osteobl	bone
49	chr12:64603400-64614600	Weak transcription	NHLF	lung
50	chr12:64604400-64615000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links