Variant report

Variant	rs1165674
Chromosome Location	chr12:104320597-104320598
allele	C/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:5)
LncRNA
region (count:0)
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	POLR2A	chr12:104320182-104320958	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:104320197-104321725	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:104320257-104326275	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:104320260-104321787	GM12892	blood:	n/a	n/a
5	ZNF384	chr12:104320521-104320602	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:104318629..104321873-chr12:104322068..104323964,4	MCF-7	breast:
2	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
3	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
4	chr12:104300678..104303599-chr12:104319392..104323559,4	K562	blood:
5	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
ENSG00000204954	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10778305	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165668	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1165669	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165670	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165675	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866071	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576954	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576955	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583282	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467677	0.99[ASN][1000 genomes]
rs73177924	0.98[ASN][1000 genomes]
rs73177926	0.98[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	chr12:104318800-104322000	Weak transcription	NHLF	lung
8	chr12:104319000-104322000	Enhancers	Fetal Thymus	thymus
9	chr12:104319200-104321600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:104319200-104322200	Weak transcription	NHDF-Ad	bronchial
11	chr12:104319200-104322400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:104319400-104321200	Weak transcription	Thymus	Thymus
13	chr12:104319400-104321600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:104319400-104321800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:104319400-104322000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:104319400-104322000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:104319400-104322000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:104319400-104322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:104319400-104322200	Weak transcription	A549	lung
20	chr12:104319400-104322400	Weak transcription	Osteobl	bone
21	chr12:104319400-104322600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:104319400-104323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:104319600-104320600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:104319600-104321200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:104319600-104321400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:104319600-104322000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:104319600-104322000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:104319600-104322200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:104319600-104322200	Weak transcription	HMEC	breast
30	chr12:104319600-104322400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:104319600-104322400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:104319600-104322400	Weak transcription	HSMM	muscle
33	chr12:104319600-104322400	Weak transcription	NHEK	skin
34	chr12:104319600-104322600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:104319600-104322600	Weak transcription	HSMMtube	muscle
36	chr12:104319800-104322600	Weak transcription	NH-A	brain
37	chr12:104320000-104321000	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:104320200-104321200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:104320200-104321200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:104320200-104322400	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links