Variant report

Variant	rs17034911
Chromosome Location	chr12:104319683-104319684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104318814-104319708	GM12878	blood:	n/a	n/a
2	CHD1	chr12:104318985-104320023	GM12878	blood:	n/a	n/a
3	PML	chr12:104318684-104319695	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:104318890-104319686	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:104318807-104320484	GM12891	blood:	n/a	n/a
6	POLR2A	chr12:104318691-104319686	GM12878	blood:	n/a	n/a
7	JUND	chr12:104318615-104319695	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:104318629..104321873-chr12:104322068..104323964,4	MCF-7	breast:
2	chr12:104314393..104320294-chr12:104321148..104324855,10	K562	blood:
3	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
4	chr12:104317968..104319875-chr12:104322035..104323737,2	MCF-7	breast:
5	chr12:104300678..104303599-chr12:104319392..104323559,4	K562	blood:
6	chr12:104319631..104321504-chr12:104324248..104326474,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3652	TF binding region
HSP90B1	TF binding region
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000204954	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10778306	0.83[ASN][1000 genomes]
rs11111845	0.83[ASN][1000 genomes]
rs12426161	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12427041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582800	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17034880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034946	1.00[AFR][1000 genomes]
rs17795947	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1882019	1.00[AFR][1000 genomes]
rs3751207	1.00[AFR][1000 genomes]
rs3751208	1.00[AFR][1000 genomes]
rs3829300	1.00[AFR][1000 genomes]
rs4135060	1.00[AFR][1000 genomes]
rs4135076	1.00[AFR][1000 genomes]
rs4135078	1.00[AFR][1000 genomes]
rs4135082	1.00[AFR][1000 genomes]
rs4135085	1.00[AFR][1000 genomes]
rs4135086	1.00[AFR][1000 genomes]
rs4135087	1.00[AFR][1000 genomes]
rs4135094	1.00[AFR][1000 genomes]
rs4135095	1.00[AFR][1000 genomes]
rs55919036	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56040534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59879726	0.82[ASN][1000 genomes]
rs60534873	1.00[AFR][1000 genomes]
rs6615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728167	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9788014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104306200-104320800	Weak transcription	Psoas Muscle	Psoas
2	chr12:104317200-104322600	Weak transcription	Aorta	Aorta
3	chr12:104317400-104322200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:104318000-104322400	Weak transcription	Brain Substantia Nigra	brain
5	chr12:104318200-104321400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:104318200-104322200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:104318600-104319800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:104318800-104319800	Enhancers	NH-A	brain
9	chr12:104318800-104322000	Weak transcription	NHLF	lung
10	chr12:104319000-104320200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:104319000-104320200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:104319000-104322000	Enhancers	Fetal Thymus	thymus
13	chr12:104319200-104321600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:104319200-104322200	Weak transcription	NHDF-Ad	bronchial
15	chr12:104319200-104322400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:104319400-104321200	Weak transcription	Thymus	Thymus
17	chr12:104319400-104321600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:104319400-104321800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:104319400-104322000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:104319400-104322000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:104319400-104322000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:104319400-104322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:104319400-104322200	Weak transcription	A549	lung
24	chr12:104319400-104322400	Weak transcription	Osteobl	bone
25	chr12:104319400-104322600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:104319400-104323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:104319600-104319800	Flanking Active TSS	GM12878-XiMat	blood
28	chr12:104319600-104320600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:104319600-104321200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:104319600-104321400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:104319600-104322000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:104319600-104322000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:104319600-104322200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:104319600-104322200	Weak transcription	HMEC	breast
35	chr12:104319600-104322400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:104319600-104322400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:104319600-104322400	Weak transcription	HSMM	muscle
38	chr12:104319600-104322400	Weak transcription	NHEK	skin
39	chr12:104319600-104322600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:104319600-104322600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links