Variant report

Variant	rs13387842
Chromosome Location	chr2:37876476-37876477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:37867842-37879116	U87	brain:	n/a	n/a
2	POLR2A	chr2:37874506-37876510	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:37876302-37877024	SK-N-SH	brain:	n/a	n/a
4	ZNF384	chr2:37876420-37876777	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:37874389-37877120	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:37874425-37878298	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:37872360-37878906	U87	brain:	n/a	n/a
8	POLR2A	chr2:37874456-37876500	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
CDC42EP3	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1013291	0.88[ASN][1000 genomes]
rs1013292	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10694	0.95[ASN][1000 genomes]
rs11124594	0.81[EUR][1000 genomes]
rs11124595	0.80[EUR][1000 genomes]
rs11883958	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12622958	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13392288	0.88[ASN][1000 genomes]
rs13406302	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417957	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1468663	0.88[ASN][1000 genomes]
rs1468664	0.88[ASN][1000 genomes]
rs17021174	0.91[ASN][1000 genomes]
rs2041508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072419	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2079998	0.88[ASN][1000 genomes]
rs2098198	0.88[ASN][1000 genomes]
rs2109821	0.88[ASN][1000 genomes]
rs2109822	0.88[ASN][1000 genomes]
rs2159726	0.88[ASN][1000 genomes]
rs2191841	0.88[ASN][1000 genomes]
rs2373290	0.88[ASN][1000 genomes]
rs2373292	0.81[AMR][1000 genomes]
rs3731852	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731854	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4372883	0.88[ASN][1000 genomes]
rs4594425	0.88[ASN][1000 genomes]
rs4670210	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670211	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4670748	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56809883	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544095	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67084656	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709067	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709621	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6711909	0.84[ASN][1000 genomes]
rs6722589	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740127	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6752119	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6752220	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752762	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759224	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607934	0.80[EUR][1000 genomes]
rs7735	0.95[ASN][1000 genomes]
rs9742	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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 target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:37870800-37878600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
12	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
13	chr2:37873000-37881400	Enhancers	Right Atrium	heart
14	chr2:37873200-37877200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:37873400-37876800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:37873600-37876800	Weak transcription	Pancreas	Pancrea
17	chr2:37873600-37879600	Weak transcription	Gastric	stomach
18	chr2:37873600-37879600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:37873600-37880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:37873600-37881000	Weak transcription	Ovary	ovary
21	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:37874200-37881600	Genic enhancers	NHLF	lung
23	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
24	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
25	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
26	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:37874800-37876800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:37874800-37880000	Genic enhancers	Lung	lung
29	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
30	chr2:37875000-37876800	Enhancers	Esophagus	oesophagus
31	chr2:37875000-37878600	Genic enhancers	HMEC	breast
32	chr2:37875200-37876600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr2:37875200-37877000	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:37875200-37877800	Enhancers	Fetal Heart	heart
35	chr2:37875200-37878000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:37875200-37879400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:37875200-37881800	Enhancers	Spleen	Spleen
38	chr2:37875200-37882200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:37875400-37877400	Weak transcription	NHEK	skin
40	chr2:37875400-37877600	Enhancers	HUVEC	blood vessel
41	chr2:37875400-37879400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:37875400-37881200	Enhancers	Primary B cells from peripheral blood	blood
43	chr2:37875400-37883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:37875600-37876600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:37875600-37877000	Enhancers	Fetal Thymus	thymus
46	chr2:37875600-37878200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:37875600-37879200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:37875600-37881000	Weak transcription	Fetal Brain Female	brain
49	chr2:37875600-37881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:37875800-37876600	Enhancers	Primary T cells from cord blood	blood

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