Variant report

Variant	rs590166
Chromosome Location	chr12:74935833-74935834
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 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	chr12:74931110-74940575	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:74934609-74936061	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:74934898-74938452	K562	blood:	n/a	n/a
5	POLR2A	chr12:74932912-74937655	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:74934609-74937472	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:74931035-74936789	IMR90	lung:	n/a	n/a
8	POLR2A	chr12:74932414-74936105	A549	lung:	n/a	n/a
9	POLR2A	chr12:74931091-74937173	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:74935783-74936039	ProgFib	skin:	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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1037887	1.00[AFR][1000 genomes]
rs1389486	0.83[AFR][1000 genomes]
rs1389487	0.83[AFR][1000 genomes]
rs1389489	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1389490	1.00[AFR][1000 genomes]
rs1389491	1.00[AFR][1000 genomes]
rs1493798	1.00[AFR][1000 genomes]
rs1493804	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1493807	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1563930	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1870699	1.00[AFR][1000 genomes]
rs1873987	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1873988	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2007674	1.00[AFR][1000 genomes]
rs2029717	1.00[AFR][1000 genomes]
rs2219608	1.00[AFR][1000 genomes]
rs2249335	0.83[AFR][1000 genomes]
rs2252250	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2605360	1.00[AFR][1000 genomes]
rs2605379	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2605380	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613880	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613892	1.00[AFR][1000 genomes]
rs2613896	1.00[AFR][1000 genomes]
rs2613899	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2641465	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2925223	1.00[AFR][1000 genomes]
rs2925224	1.00[AFR][1000 genomes]
rs2926807	1.00[AFR][1000 genomes]
rs588875	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs596999	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs625531	1.00[AFR][1000 genomes]
rs663854	1.00[AFR][1000 genomes]
rs694314	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs822806	1.00[YRI][hapmap]
rs822809	1.00[YRI][hapmap]
rs922222	0.83[AFR][1000 genomes]
rs970236	1.00[AFR][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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74932800-74936600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:74933200-74936000	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr12:74933800-74936000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:74933800-74936200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:74933800-74937000	Weak transcription	Esophagus	oesophagus
6	chr12:74933800-74942800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:74934000-74936000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:74934000-74936200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:74934200-74936000	Genic enhancers	HSMM	muscle
10	chr12:74934200-74936200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:74934200-74936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:74934200-74942000	Weak transcription	Ovary	ovary
13	chr12:74934400-74938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:74934600-74936200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:74934600-74937600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:74934600-74937600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:74934600-74940800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:74934800-74936000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:74934800-74936200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:74934800-74936800	Genic enhancers	Primary B cells from cord blood	blood
21	chr12:74935000-74936000	Weak transcription	Aorta	Aorta
22	chr12:74935000-74936200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:74935000-74936200	Genic enhancers	Primary T cells from cord blood	blood
24	chr12:74935000-74936400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:74935000-74936400	Genic enhancers	Liver	Liver
26	chr12:74935000-74936600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:74935000-74937000	Weak transcription	Brain Angular Gyrus	brain
28	chr12:74935200-74936000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:74935200-74936000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:74935200-74936000	Strong transcription	Fetal Intestine Large	intestine
31	chr12:74935200-74936000	Enhancers	Fetal Lung	lung
32	chr12:74935200-74936000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:74935200-74936200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:74935200-74936200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:74935200-74936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:74935200-74936200	Strong transcription	Fetal Thymus	thymus
37	chr12:74935200-74936200	Genic enhancers	Dnd41	blood
38	chr12:74935200-74936400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:74935200-74936600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:74935200-74936600	Enhancers	Brain Cingulate Gyrus	brain
41	chr12:74935200-74936800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:74935200-74936800	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:74935200-74936800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:74935200-74937600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:74935200-74938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:74935200-74940800	Weak transcription	Pancreas	Pancrea
47	chr12:74935200-74941000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:74935200-74941800	Weak transcription	Thymus	Thymus
49	chr12:74935200-74942200	Weak transcription	Psoas Muscle	Psoas
50	chr12:74935200-74942600	Weak transcription	Small Intestine	intestine

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