Variant report

Variant	rs58852079
Chromosome Location	chr12:56706922-56706923
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56706868-56707262	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56705654..56712950-chr12:56716015..56720160,8	MCF-7	breast:
2	chr12:56690986..56698275-chr12:56706607..56711958,20	MCF-7	breast:
3	chr12:56700910..56706653-chr12:56706710..56711113,8	K562	blood:
4	chr12:56703600..56706626-chr12:56706710..56710673,5	K562	blood:
5	chr12:56690402..56700610-chr12:56705161..56712229,20	K562	blood:

No data

Variant related genes	Relation type
CNPY2	TF binding region
ENSG00000257303	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000257740	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257727	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10876882	0.81[EUR][1000 genomes]
rs11171803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575234	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274490	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295772	0.91[ASN][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17118439	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2020854	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629447	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643623	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643626	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695782	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695789	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41392645	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542959	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773652	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773664	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773665	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808919	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs58852079	RP11-977G19.11	cis	Artery Aorta	GTEx
rs58852079	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs58852079	RP11-977G19.11	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56694600-56708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:56694800-56708200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:56694800-56708800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:56695000-56708000	Weak transcription	Fetal Brain Male	brain
5	chr12:56695000-56708600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:56695600-56708000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:56695600-56708200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:56695600-56708600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:56695800-56708000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:56695800-56708000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:56696000-56708200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:56696200-56708200	Strong transcription	Fetal Intestine Small	intestine
13	chr12:56696200-56708400	Strong transcription	Fetal Stomach	stomach
14	chr12:56696400-56707000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:56696400-56708000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:56696400-56708200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:56696400-56708200	Weak transcription	Stomach Mucosa	stomach
18	chr12:56696400-56708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:56696400-56708600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:56696600-56708400	Strong transcription	Fetal Thymus	thymus
21	chr12:56696800-56708200	Strong transcription	Fetal Intestine Large	intestine
22	chr12:56697000-56708000	Weak transcription	Fetal Heart	heart
23	chr12:56697000-56708400	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:56697200-56708200	Strong transcription	Fetal Brain Female	brain
25	chr12:56697200-56708400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:56697200-56708400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:56697200-56708600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:56697400-56707000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:56697600-56708000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:56697800-56708200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:56697800-56708200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:56697800-56708200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:56697800-56708400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:56697800-56708400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:56697800-56708400	Strong transcription	Osteobl	bone
36	chr12:56697800-56708600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:56697800-56708600	Strong transcription	Placenta	Placenta
38	chr12:56698000-56708200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:56698000-56708600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:56698000-56708600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:56698200-56708400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:56698200-56708400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:56698400-56708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:56698800-56708200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:56699200-56707000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:56699200-56707200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:56700200-56708400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:56700400-56708400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:56700400-56708400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:56700400-56708400	Strong transcription	Muscle Satellite Cultured Cells	--

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