Variant report

Variant	rs13013245
Chromosome Location	chr2:46806086-46806087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1001745	1.00[CHB][hapmap]
rs12997164	1.00[CHB][hapmap]
rs13000560	0.90[EUR][1000 genomes]
rs13032670	0.92[ASN][1000 genomes]
rs13033177	0.92[ASN][1000 genomes]
rs17818315	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17819022	1.00[JPT][hapmap]
rs2122715	1.00[JPT][hapmap]
rs34050156	0.81[EUR][1000 genomes]
rs35350086	0.89[ASN][1000 genomes]
rs35625984	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35870739	0.88[EUR][1000 genomes]
rs4142759	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4952831	1.00[CHB][hapmap]
rs4952833	1.00[CHB][hapmap]
rs4952834	1.00[CHB][hapmap]
rs4953401	0.86[ASN][1000 genomes]
rs56086832	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62134741	0.86[EUR][1000 genomes]
rs62134759	0.88[EUR][1000 genomes]
rs7607308	1.00[CHB][hapmap]
rs7607633	1.00[CHB][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13013245	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs13013245	CRIPT	cis	multi-tissue	Pritchard
rs13013245	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13013245	CRIPT	cis	Temporal Cortex	GTEx
rs13013245	ATP6V1E2	cis	Esophagus Muscularis	GTEx
rs13013245	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs13013245	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs13013245	CRIPT	cis	Frontal Cortex	GTEx

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	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
3	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:46787800-46806600	Weak transcription	Gastric	stomach
9	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
10	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:46790600-46806200	Weak transcription	Dnd41	blood
16	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
17	chr2:46793000-46806400	Weak transcription	Lung	lung
18	chr2:46793200-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:46793200-46806200	Weak transcription	Aorta	Aorta
20	chr2:46796000-46807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:46796200-46806400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:46796200-46807800	Weak transcription	Stomach Mucosa	stomach
24	chr2:46796400-46806400	Weak transcription	Placenta	Placenta
25	chr2:46796400-46807000	Weak transcription	Spleen	Spleen
26	chr2:46796600-46807200	Weak transcription	Pancreas	Pancrea
27	chr2:46796600-46807400	Weak transcription	Thymus	Thymus
28	chr2:46796600-46822000	Weak transcription	Fetal Brain Male	brain
29	chr2:46796800-46807400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
31	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:46797200-46806400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:46797800-46814400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:46797800-46841000	Weak transcription	K562	blood
35	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:46798400-46807200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:46798600-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:46798800-46806600	Weak transcription	Liver	Liver
39	chr2:46798800-46807400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:46799600-46806600	Weak transcription	Fetal Intestine Small	intestine
41	chr2:46799800-46806600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:46800200-46807000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:46800600-46807000	Weak transcription	Ovary	ovary
44	chr2:46801200-46808400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:46801200-46815000	Weak transcription	Psoas Muscle	Psoas
46	chr2:46801400-46807000	Weak transcription	Fetal Intestine Large	intestine
47	chr2:46801600-46807400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:46801800-46806200	Weak transcription	Fetal Stomach	stomach
49	chr2:46802400-46806400	Weak transcription	HSMMtube	muscle
50	chr2:46802400-46807000	Weak transcription	Brain Cingulate Gyrus	brain

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