Variant report

Variant	rs13403918
Chromosome Location	chr2:128024952-128024953
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	chr2:128024843-128025265	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:128022890..128025084-chr2:128050178..128052687,2	K562	blood:
2	chr2:128023731..128026474-chr2:128028520..128030504,2	K562	blood:
3	chr2:128023647..128026274-chr2:128041250..128043477,2	K562	blood:

Variant related genes	Relation type
ERCC3	TF binding region
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10167294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928764	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1143407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684068	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613252	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613413	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614320	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619391	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017103	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034157	0.84[EUR][1000 genomes]
rs13390029	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13409933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414676	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429925	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139142	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276682	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276683	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28807127	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088374	0.87[ASN][1000 genomes]
rs34006114	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34441363	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34487399	0.92[EUR][1000 genomes]
rs34601617	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34703177	0.91[EUR][1000 genomes]
rs35708549	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738948	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893313	0.94[EUR][1000 genomes]
rs4150434	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150492	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150514	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300780	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359587	0.94[EUR][1000 genomes]
rs4528711	0.88[EUR][1000 genomes]
rs4662721	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4662724	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58063879	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59027829	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6430937	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716392	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735779	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738811	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6747862	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752139	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67771362	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584659	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9752366	0.85[EUR][1000 genomes]
rs9923	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs13403918	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13403918	AC068282.3	cis	lung	GTEx
rs13403918	MAP3K2	cis	multi-tissue	Pritchard
rs13403918	AC068282.3	cis	Esophagus Mucosa	GTEx
rs13403918	AC068282.3	cis	Artery Tibial	GTEx
rs13403918	AC068282.3	cis	Artery Aorta	GTEx
rs13403918	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs13403918	AC068282.3	cis	Stomach	GTEx
rs13403918	AC068282.3	cis	Muscle Skeletal	GTEx
rs13403918	AC068282.3	cis	Esophagus Muscularis	GTEx
rs13403918	AC068282.3	cis	Whole Blood	GTEx
rs13403918	AC068282.3	cis	Heart Left Ventricle	GTEx
rs13403918	AC068282.3	cis	Nerve Tibial	GTEx
rs13403918	AC068282.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128012400-128028000	Weak transcription	Hela-S3	cervix
2	chr2:128012600-128026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:128013600-128036200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:128014000-128041000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:128014600-128041000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:128016200-128027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:128017200-128027400	Weak transcription	Esophagus	oesophagus
8	chr2:128017400-128025000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:128017600-128026400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:128017600-128027800	Weak transcription	Small Intestine	intestine
11	chr2:128018200-128025600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:128018800-128025000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:128018800-128025000	Weak transcription	Right Ventricle	heart
14	chr2:128018800-128025200	Weak transcription	Gastric	stomach
15	chr2:128018800-128025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:128018800-128025800	Weak transcription	Spleen	Spleen
17	chr2:128019000-128025200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:128019000-128025200	Weak transcription	Aorta	Aorta
19	chr2:128019000-128025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:128019000-128025800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:128019000-128025800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:128019000-128025800	Weak transcription	Psoas Muscle	Psoas
23	chr2:128019000-128026200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:128019000-128026200	Weak transcription	NHEK	skin
25	chr2:128019000-128027400	Weak transcription	Fetal Brain Male	brain
26	chr2:128019000-128027400	Weak transcription	Pancreas	Pancrea
27	chr2:128019000-128027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:128019000-128028200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:128019000-128028200	Weak transcription	NHLF	lung
30	chr2:128019200-128025000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:128019200-128026000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:128019200-128026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:128019400-128025200	Weak transcription	Colonic Mucosa	Colon
34	chr2:128019400-128027800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:128019400-128028000	Weak transcription	K562	blood
36	chr2:128019600-128025000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:128019600-128025200	Weak transcription	GM12878-XiMat	blood
38	chr2:128019800-128025800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:128019800-128026200	Weak transcription	Fetal Heart	heart
40	chr2:128020000-128025800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:128020000-128025800	Weak transcription	Lung	lung
42	chr2:128020200-128025000	Weak transcription	Brain Angular Gyrus	brain
43	chr2:128020200-128025200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:128020200-128025400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:128020200-128028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:128020400-128025000	Weak transcription	Brain Germinal Matrix	brain
47	chr2:128020600-128025000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:128020800-128025000	Weak transcription	HSMM	muscle
49	chr2:128020800-128025200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:128020800-128025200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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