Variant report

Variant	rs7309292
Chromosome Location	chr12:124083616-124083617
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr12:124083231-124083741	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:124083541-124084062	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:124082990-124083946	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:124082873-124083645	K562	blood:	n/a	n/a
5	POLR2A	chr12:124082972-124084214	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:124082678-124084635	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:124083359-124084090	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:124081632-124084546	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:124082928-124083676	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:124082980-124083698	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:124083320-124083869	K562	blood:	n/a	n/a
12	POLR2A	chr12:124082936-124084130	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:124083294-124083659	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:124082859-124084959	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr12:124082946-124084499	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:124083030-124084509	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:124080492-124084849	K562	blood:	n/a	n/a
18	POLR2A	chr12:124083004-124084250	GM12891	blood:	n/a	n/a
19	POLR2A	chr12:124083209-124083831	HL-60	blood:	n/a	n/a
20	POLR2A	chr12:124082907-124084808	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr12:124082908-124084597	GM12891	blood:	n/a	n/a
22	POLR2A	chr12:124082865-124084612	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr12:124082950-124084340	U87	brain:	n/a	n/a
24	POLR2A	chr12:124083537-124084305	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr12:124082857-124085456	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:124083355-124084361	U87	brain:	n/a	n/a
27	POLR2A	chr12:124083513-124083772	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:124065661..124069328-chr12:124081746..124084446,4	K562	blood:
2	chr12:124081195..124083992-chr12:124117533..124119708,3	MCF-7	breast:
3	chr12:124075051..124078239-chr12:124079848..124084285,5	K562	blood:
4	chr12:123752131..123754716-chr12:124081309..124084264,2	MCF-7	breast:
5	chr12:124069965..124078255-chr12:124078837..124084347,12	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111361	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1050443	0.92[EUR][1000 genomes]
rs1050448	0.84[EUR][1000 genomes]
rs1050449	0.84[EUR][1000 genomes]
rs1056132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057301	0.83[EUR][1000 genomes]
rs11833889	0.88[EUR][1000 genomes]
rs12809853	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816883	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12829500	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15587	0.88[EUR][1000 genomes]
rs16917551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3190835	0.85[EUR][1000 genomes]
rs3204541	0.88[EUR][1000 genomes]
rs34097324	0.88[EUR][1000 genomes]
rs34369761	0.82[EUR][1000 genomes]
rs34514002	0.87[EUR][1000 genomes]
rs35064645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708602	0.88[EUR][1000 genomes]
rs35867744	0.88[EUR][1000 genomes]
rs36002329	0.99[EUR][1000 genomes]
rs3850952	0.81[EUR][1000 genomes]
rs4930704	0.86[ASN][1000 genomes]
rs4930709	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930713	0.83[EUR][1000 genomes]
rs4930714	0.83[EUR][1000 genomes]
rs55705511	0.85[EUR][1000 genomes]
rs56213464	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56675602	0.88[EUR][1000 genomes]
rs59126974	0.87[EUR][1000 genomes]
rs6488877	0.86[ASN][1000 genomes]
rs6488884	0.84[EUR][1000 genomes]
rs66494087	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66694750	0.88[EUR][1000 genomes]
rs68163141	0.86[EUR][1000 genomes]
rs7137473	0.87[EUR][1000 genomes]
rs7139162	0.87[EUR][1000 genomes]
rs71458807	0.93[EUR][1000 genomes]
rs71458808	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308304	0.88[EUR][1000 genomes]
rs7313207	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313751	0.86[ASN][1000 genomes]
rs7398935	0.86[ASN][1000 genomes]
rs7953876	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956299	0.86[ASN][1000 genomes]
rs7962151	0.86[ASN][1000 genomes]
rs7963804	0.86[ASN][1000 genomes]
rs7972380	0.83[EUR][1000 genomes]
rs7973766	0.82[EUR][1000 genomes]
rs7979561	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7309292	TCTN2	cis	Artery Tibial	GTEx
rs7309292	TCTN2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124071200-124083800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:124071200-124083800	Strong transcription	Placenta	Placenta
5	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
10	chr12:124072400-124083800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:124073400-124084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:124073600-124083800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:124073600-124083800	Strong transcription	Left Ventricle	heart
16	chr12:124073800-124083800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:124073800-124083800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:124073800-124084200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:124073800-124084600	Strong transcription	Fetal Thymus	thymus
20	chr12:124073800-124085200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:124073800-124085400	Weak transcription	Stomach Mucosa	stomach
22	chr12:124074000-124083800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:124074000-124084400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:124074200-124086000	Weak transcription	Fetal Heart	heart
25	chr12:124075000-124084000	Strong transcription	Brain Substantia Nigra	brain
26	chr12:124075000-124084200	Strong transcription	Dnd41	blood
27	chr12:124075200-124085600	Weak transcription	Right Ventricle	heart
28	chr12:124075200-124085800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:124075200-124086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:124075200-124086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:124076800-124083800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:124076800-124084000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:124076800-124085600	Weak transcription	Pancreas	Pancrea
34	chr12:124077000-124083800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:124077000-124085600	Weak transcription	Spleen	Spleen
36	chr12:124077000-124086200	Weak transcription	Aorta	Aorta
37	chr12:124077200-124083800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:124077200-124083800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:124077400-124083800	Strong transcription	Osteobl	bone
40	chr12:124077400-124086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:124077400-124086000	Weak transcription	Fetal Brain Male	brain
42	chr12:124078400-124085600	Weak transcription	Esophagus	oesophagus
43	chr12:124078600-124085200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:124078600-124085400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:124078800-124084200	Strong transcription	HSMM	muscle
46	chr12:124079000-124084200	Strong transcription	Fetal Lung	lung
47	chr12:124079000-124084400	Strong transcription	Primary T cells from cord blood	blood
48	chr12:124079400-124085400	Weak transcription	Fetal Intestine Small	intestine
49	chr12:124079400-124085600	Weak transcription	Fetal Stomach	stomach
50	chr12:124079400-124085600	Weak transcription	Lung	lung

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