Variant report

Variant	rs647129
Chromosome Location	chr12:74935652-74935653
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:74931200-74936073	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:74935499-74935657	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:74931110-74940575	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:74931116-74935658	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:74934609-74936061	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:74934898-74938452	K562	blood:	n/a	n/a
7	POLR2A	chr12:74932912-74937655	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:74934609-74937472	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:74931035-74936789	IMR90	lung:	n/a	n/a
10	POLR2A	chr12:74932414-74936105	A549	lung:	n/a	n/a
11	POLR2A	chr12:74931091-74937173	GM12891	blood:	n/a	n/a
12	EBF1	chr12:74935630-74935742	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:74934644..74937630-chr12:74950063..74952451,3	MCF-7	breast:
2	chr12:74819585..74822514-chr12:74935420..74937697,2	K562	blood:
3	chr12:74934002..74935915-chr12:74937667..74942932,5	K562	blood:
4	chr12:74933499..74938752-chr12:74938991..74943644,10	K562	blood:
5	chr12:74934893..74937822-chr12:74975475..74977928,2	MCF-7	breast:
6	chr12:74920482..74922543-chr12:74935619..74938584,2	MCF-7	breast:
7	chr12:74929601..74933992-chr12:74933997..74938801,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257386	TF binding region
ENSG00000257386	Chromatin interaction
ENSG00000253719	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10785126	0.83[ASN][1000 genomes]
rs10879793	0.83[ASN][1000 genomes]
rs11180097	0.83[AFR][1000 genomes]
rs12816388	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1389492	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1461048	0.83[ASN][1000 genomes]
rs1493797	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1493805	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1493806	0.82[ASN][1000 genomes]
rs2605330	0.83[ASN][1000 genomes]
rs2605338	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605376	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2605377	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2613882	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2613888	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2613895	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2613900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2613901	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2613903	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2641467	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2641468	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2641481	0.82[ASN][1000 genomes]
rs597888	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628576	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8744	0.95[AMR][1000 genomes];0.82[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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74932600-74935800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
2	chr12:74932800-74936600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:74933200-74936000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr12:74933800-74936000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:74933800-74936200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:74933800-74937000	Weak transcription	Esophagus	oesophagus
7	chr12:74933800-74942800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:74934000-74936000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:74934000-74936200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:74934200-74936000	Genic enhancers	HSMM	muscle
11	chr12:74934200-74936200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:74934200-74936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:74934200-74942000	Weak transcription	Ovary	ovary
14	chr12:74934400-74938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:74934600-74935800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:74934600-74935800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:74934600-74936200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:74934600-74937600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:74934600-74937600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:74934600-74940800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:74934800-74935800	Enhancers	Fetal Brain Male	brain
22	chr12:74934800-74935800	Enhancers	Fetal Heart	heart
23	chr12:74934800-74935800	Genic enhancers	Osteobl	bone
24	chr12:74934800-74936000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:74934800-74936200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr12:74934800-74936800	Genic enhancers	Primary B cells from cord blood	blood
27	chr12:74935000-74935800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
28	chr12:74935000-74935800	Genic enhancers	NH-A	brain
29	chr12:74935000-74936000	Weak transcription	Aorta	Aorta
30	chr12:74935000-74936200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:74935000-74936200	Genic enhancers	Primary T cells from cord blood	blood
32	chr12:74935000-74936400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:74935000-74936400	Genic enhancers	Liver	Liver
34	chr12:74935000-74936600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:74935000-74937000	Weak transcription	Brain Angular Gyrus	brain
36	chr12:74935200-74935800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:74935200-74935800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:74935200-74935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:74935200-74935800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:74935200-74935800	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr12:74935200-74935800	Strong transcription	Fetal Muscle Leg	muscle
42	chr12:74935200-74935800	Strong transcription	Hela-S3	cervix
43	chr12:74935200-74936000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:74935200-74936000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:74935200-74936000	Strong transcription	Fetal Intestine Large	intestine
46	chr12:74935200-74936000	Enhancers	Fetal Lung	lung
47	chr12:74935200-74936000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:74935200-74936200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:74935200-74936200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:74935200-74936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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