Variant report

Variant	rs13024414
Chromosome Location	chr2:46687062-46687063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46673194..46677108-chr2:46685172..46689084,4	MCF-7	breast:
2	chr2:46524557..46526648-chr2:46685519..46687325,2	MCF-7	breast:
3	chr2:46654324..46657409-chr2:46685735..46688601,3	K562	blood:

Variant related genes	Relation type
ENSG00000241791	Chromatin interaction
ENSG00000116016	Chromatin interaction
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12986899	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13002880	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003074	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13020043	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530621	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530624	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1597040	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900591	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2121698	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2121700	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34854267	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35509718	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36006825	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4312543	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4396767	0.86[EUR][1000 genomes]
rs4549147	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563285	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4953379	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6544895	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6718875	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749877	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6757564	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718849	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7565188	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7565770	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	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
8	nsv581745	chr2:46660445-46693963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13024414	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13024414	ATP6V1E2	cis	Muscle Skeletal	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:46679000-46687400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46680600-46687200	Weak transcription	Stomach Mucosa	stomach
4	chr2:46684000-46688000	Weak transcription	K562	blood
5	chr2:46684200-46687400	Weak transcription	Placenta	Placenta
6	chr2:46684800-46687600	Enhancers	HepG2	liver
7	chr2:46685800-46688400	Enhancers	Stomach Smooth Muscle	stomach
8	chr2:46685800-46688600	Enhancers	Fetal Stomach	stomach
9	chr2:46686000-46687200	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:46686000-46687200	Enhancers	Brain Substantia Nigra	brain
11	chr2:46686000-46687400	Enhancers	Brain Anterior Caudate	brain
12	chr2:46686000-46687400	Enhancers	Brain Hippocampus Middle	brain
13	chr2:46686000-46687800	Enhancers	Fetal Kidney	kidney
14	chr2:46686000-46688200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:46686000-46688600	Enhancers	Fetal Lung	lung
16	chr2:46686000-46689000	Enhancers	Adipose Nuclei	Adipose
17	chr2:46686200-46687200	Enhancers	Brain Angular Gyrus	brain
18	chr2:46686200-46687200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:46686200-46688600	Enhancers	Fetal Muscle Leg	muscle
20	chr2:46686200-46688800	Enhancers	Fetal Muscle Trunk	muscle
21	chr2:46686400-46687200	Weak transcription	Left Ventricle	heart
22	chr2:46686400-46687200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:46686400-46687400	Weak transcription	Ovary	ovary
24	chr2:46686400-46687400	Weak transcription	Spleen	Spleen
25	chr2:46686400-46688600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:46686400-46688600	Enhancers	Colon Smooth Muscle	Colon
27	chr2:46686400-46689000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:46686400-46689000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:46686400-46689000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:46686400-46689200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:46686400-46689200	Enhancers	Right Atrium	heart
32	chr2:46686400-46689400	Enhancers	Lung	lung
33	chr2:46686400-46704400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:46686600-46687400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:46686600-46687800	Weak transcription	Colonic Mucosa	Colon
36	chr2:46686600-46688000	Enhancers	Esophagus	oesophagus
37	chr2:46686600-46688400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:46686600-46688600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:46686600-46688600	Enhancers	Fetal Intestine Large	intestine
40	chr2:46686600-46689000	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:46686600-46689000	Enhancers	NHLF	lung
42	chr2:46686800-46687200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:46686800-46688600	Enhancers	Fetal Heart	heart
44	chr2:46686800-46691600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:46687000-46687400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:46687000-46689000	Enhancers	Pancreas	Pancrea
47	chr2:46687000-46689200	Enhancers	Hela-S3	cervix

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