Variant report

Variant	rs13404342
Chromosome Location	chr2:46805373-46805374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1057899	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11306	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11901678	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11903907	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13410076	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1376406	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1456018	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17035272	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035361	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1809087	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs3213985	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3768724	0.86[EUR][1000 genomes]
rs3768725	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4377377	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57134465	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57955462	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58101879	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58342271	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59183773	0.87[ASN][1000 genomes]
rs59823825	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60199254	0.86[EUR][1000 genomes]
rs60211996	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60738814	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61252474	0.87[ASN][1000 genomes]
rs6544904	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544908	0.83[EUR][1000 genomes]
rs6713104	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6719813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6727471	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6733143	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6749372	0.86[EUR][1000 genomes]
rs6756134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs68104662	0.86[ASN][1000 genomes]
rs72875696	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563577	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7589908	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591561	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592446	0.81[ASN][1000 genomes]
rs962467	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808496	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13404342	CRIPT	cis	multi-tissue	Pritchard
rs13404342	ATP6V1E2	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
4	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
5	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:46787800-46806600	Weak transcription	Gastric	stomach
10	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
11	chr2:46789800-46805800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:46790600-46806200	Weak transcription	Dnd41	blood
18	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
19	chr2:46793000-46806400	Weak transcription	Lung	lung
20	chr2:46793200-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:46793200-46806200	Weak transcription	Aorta	Aorta
22	chr2:46796000-46807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:46796200-46806400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:46796200-46807800	Weak transcription	Stomach Mucosa	stomach
26	chr2:46796400-46806400	Weak transcription	Placenta	Placenta
27	chr2:46796400-46807000	Weak transcription	Spleen	Spleen
28	chr2:46796600-46807200	Weak transcription	Pancreas	Pancrea
29	chr2:46796600-46807400	Weak transcription	Thymus	Thymus
30	chr2:46796600-46822000	Weak transcription	Fetal Brain Male	brain
31	chr2:46796800-46806000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:46796800-46807400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
34	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:46797200-46806400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:46797800-46814400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:46797800-46841000	Weak transcription	K562	blood
38	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:46798400-46807200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:46798600-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:46798800-46806600	Weak transcription	Liver	Liver
42	chr2:46798800-46807400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:46799600-46806600	Weak transcription	Fetal Intestine Small	intestine
44	chr2:46799800-46806600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:46800200-46807000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:46800600-46807000	Weak transcription	Ovary	ovary
47	chr2:46801200-46808400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:46801200-46815000	Weak transcription	Psoas Muscle	Psoas
49	chr2:46801400-46807000	Weak transcription	Fetal Intestine Large	intestine
50	chr2:46801600-46807400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links