Variant report

Variant	rs62134741
Chromosome Location	chr2:46782189-46782190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46780336..46782710-chr2:46791524..46793120,2	K562	blood:
2	chr2:46781985..46785151-chr2:46792596..46794911,4	MCF-7	breast:
3	chr2:46774785..46776728-chr2:46780493..46783223,2	MCF-7	breast:
4	chr2:46769633..46771937-chr2:46780333..46785033,5	MCF-7	breast:
5	chr2:46780322..46782811-chr2:46783470..46785498,2	K562	blood:
6	chr2:46688652..46689180-chr2:46781896..46782657,2	K562	blood:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1001745	0.89[ASN][1000 genomes]
rs12997164	0.85[ASN][1000 genomes]
rs13000560	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13008088	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013245	0.86[EUR][1000 genomes]
rs13020299	0.83[ASN][1000 genomes]
rs17818315	0.86[EUR][1000 genomes]
rs34050156	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34416415	0.89[ASN][1000 genomes]
rs35178974	0.87[ASN][1000 genomes]
rs35625984	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35870739	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4142759	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952831	0.81[ASN][1000 genomes]
rs4952833	0.81[ASN][1000 genomes]
rs4952834	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56086832	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62134736	0.87[ASN][1000 genomes]
rs62134759	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607308	0.85[ASN][1000 genomes]
rs7607633	0.85[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	nsv9713	chr2:46775356-46790566	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs62134741	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs62134741	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs62134741	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs62134741	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs62134741	ATP6V1E2	cis	lung	GTEx
rs62134741	ATP6V1E2	cis	Esophagus Muscularis	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	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
4	chr2:46771800-46782400	Weak transcription	HMEC	breast
5	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
6	chr2:46772000-46782600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:46772200-46804000	Weak transcription	NH-A	brain
8	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:46774400-46782200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46774800-46789200	Weak transcription	Pancreas	Pancrea
11	chr2:46775200-46782400	Weak transcription	Fetal Lung	lung
12	chr2:46775200-46787200	Weak transcription	Gastric	stomach
13	chr2:46775200-46788600	Weak transcription	A549	lung
14	chr2:46775400-46782600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
16	chr2:46776400-46784800	Weak transcription	Dnd41	blood
17	chr2:46776400-46789000	Weak transcription	Primary T cells from cord blood	blood
18	chr2:46776600-46782400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:46776600-46784800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:46776600-46785000	Weak transcription	Liver	Liver
21	chr2:46776600-46785200	Weak transcription	Small Intestine	intestine
22	chr2:46776600-46786000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:46776600-46789000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:46776800-46794600	Weak transcription	Ovary	ovary
25	chr2:46777000-46782200	Weak transcription	Esophagus	oesophagus
26	chr2:46777000-46783400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:46777000-46785000	Weak transcription	HSMM	muscle
28	chr2:46777000-46788600	Weak transcription	Colonic Mucosa	Colon
29	chr2:46777000-46788800	Weak transcription	HSMMtube	muscle
30	chr2:46777000-46789200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:46777600-46785200	Weak transcription	Fetal Intestine Large	intestine
32	chr2:46778400-46782400	Weak transcription	Placenta	Placenta
33	chr2:46778400-46788600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:46778600-46782200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:46778600-46784800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:46778600-46786000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:46778800-46783000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:46779000-46790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:46779000-46790600	Weak transcription	K562	blood
40	chr2:46779400-46782400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:46779600-46782400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:46779800-46782800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:46779800-46788400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:46779800-46794600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:46780000-46782200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:46780000-46782400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:46780000-46782400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr2:46780000-46783800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:46780000-46785200	Weak transcription	Aorta	Aorta
50	chr2:46780000-46785200	Weak transcription	Fetal Intestine Small	intestine

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