Variant report

Variant	rs13000560
Chromosome Location	chr2:46790997-46790998
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46787456..46790451-chr2:46790520..46794497,4	K562	blood:
2	chr2:46789524..46792081-chr2:46795199..46798160,3	K562	blood:
3	chr2:46778318..46780393-chr2:46788541..46791155,3	K562	blood:
4	chr2:46778318..46780093-chr2:46788541..46791155,2	K562	blood:
5	chr2:46787456..46790384-chr2:46790520..46794497,4	K562	blood:
6	chr2:46773973..46776728-chr2:46790942..46793307,2	MCF-7	breast:
7	chr2:46790452..46793427-chr2:46811827..46814978,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13008088	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13013245	0.90[EUR][1000 genomes]
rs17818315	0.88[EUR][1000 genomes]
rs34050156	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35625984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35870739	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4142759	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952834	0.81[AMR][1000 genomes]
rs56086832	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62134741	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62134759	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13000560	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs13000560	ATP6V1E2	cis	Esophagus Muscularis	GTEx
rs13000560	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs13000560	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs13000560	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13000560	ATP6V1E2	cis	lung	GTEx

Chromatin state (count:106 , 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	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
3	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
4	chr2:46772200-46804000	Weak transcription	NH-A	brain
5	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
7	chr2:46776800-46794600	Weak transcription	Ovary	ovary
8	chr2:46779800-46794600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:46783000-46792000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:46783000-46795600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:46783000-46796800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:46783200-46791600	Weak transcription	Esophagus	oesophagus
17	chr2:46783200-46795400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:46785400-46791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:46785400-46792000	Weak transcription	Aorta	Aorta
23	chr2:46785400-46796000	Weak transcription	HSMM	muscle
24	chr2:46785400-46798400	Weak transcription	Liver	Liver
25	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:46785600-46796400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:46785800-46792600	Weak transcription	Fetal Lung	lung
30	chr2:46786000-46793000	Enhancers	Right Atrium	heart
31	chr2:46786200-46793000	Strong transcription	NHLF	lung
32	chr2:46786600-46795000	Strong transcription	Fetal Stomach	stomach
33	chr2:46786800-46791000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
35	chr2:46787200-46791600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:46787800-46806600	Weak transcription	Gastric	stomach
38	chr2:46788400-46791400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:46788400-46791600	Enhancers	Right Ventricle	heart
40	chr2:46788400-46792400	Enhancers	Colon Smooth Muscle	Colon
41	chr2:46788400-46792400	Enhancers	Psoas Muscle	Psoas
42	chr2:46788400-46792600	Genic enhancers	Fetal Thymus	thymus
43	chr2:46788400-46793400	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:46788600-46791000	Enhancers	Brain Anterior Caudate	brain
45	chr2:46788800-46791000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:46788800-46791000	Genic enhancers	Left Ventricle	heart
47	chr2:46788800-46792200	Enhancers	Brain Cingulate Gyrus	brain
48	chr2:46789000-46792600	Enhancers	Thymus	Thymus
49	chr2:46789000-46793200	Weak transcription	NHDF-Ad	bronchial
50	chr2:46789200-46791600	Weak transcription	Placenta	Placenta

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