Variant report

Variant	rs13001507
Chromosome Location	chr2:46720532-46720533
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46707494..46710484-chr2:46718946..46721502,2	K562	blood:
2	chr2:46715260..46716783-chr2:46718663..46721578,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11125075	1.00[JPT][hapmap]
rs12473626	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs12986653	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13005507	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13007688	0.83[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13008445	0.80[EUR][1000 genomes]
rs13008941	0.84[ASN][1000 genomes]
rs13010097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13014744	0.80[EUR][1000 genomes]
rs13018477	0.88[CEU][hapmap]
rs13024277	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13024546	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13025174	0.84[CEU][hapmap]
rs13025211	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13030579	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13032473	0.84[CEU][hapmap]
rs13033917	0.84[CEU][hapmap]
rs1447563	0.89[JPT][hapmap]
rs1530627	0.84[CEU][hapmap]
rs1542271	0.84[CEU][hapmap]
rs17817004	0.83[EUR][1000 genomes]
rs2084679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2121697	0.87[CEU][hapmap]
rs2121698	0.83[GIH][hapmap]
rs2121700	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs2122714	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276555	0.92[CEU][hapmap]
rs2346414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2346415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs35272216	0.84[ASN][1000 genomes]
rs3814047	0.84[CEU][hapmap]
rs4396767	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4953372	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4953385	0.84[CEU][hapmap]
rs4953387	0.83[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4953388	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953389	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4953390	0.83[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4953396	0.84[ASN][1000 genomes]
rs62134696	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134698	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6544898	0.84[EUR][1000 genomes]
rs6737959	0.84[CEU][hapmap]
rs7557998	0.83[CEU][hapmap]
rs7562332	0.88[CEU][hapmap]
rs7588938	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
9	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
10	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
11	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
12	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
13	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
14	nsv457341	chr2:46712759-46724016	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv581748	chr2:46712759-46724016	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13001507	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13001507	CRIPT	cis	lymphoblastoid	seeQTL
rs13001507	CRIPT	cis	multi-tissue	Pritchard
rs13001507	SOCS5	cis	multi-tissue	Pritchard
rs13001507	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs13001507	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs13001507	ATP6V1E2	cis	multi-tissue	Pritchard
rs13001507	CRIPT	cis	parietal	SCAN
rs13001507	ATP6V1E2	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46714800-46720800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:46718000-46722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:46718200-46720600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:46718200-46720800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:46718200-46721000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:46718200-46722600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:46718200-46726600	Weak transcription	Aorta	Aorta
9	chr2:46718400-46720600	Weak transcription	Ovary	ovary
10	chr2:46718400-46721000	Enhancers	Brain Hippocampus Middle	brain
11	chr2:46718400-46721000	Weak transcription	Right Atrium	heart
12	chr2:46718400-46726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:46718600-46720600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:46718600-46720600	Weak transcription	Fetal Brain Male	brain
15	chr2:46718600-46722000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:46718600-46722600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:46718600-46725600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:46718600-46726600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:46718600-46726600	Weak transcription	Right Ventricle	heart
20	chr2:46718800-46720800	Weak transcription	Fetal Stomach	stomach
21	chr2:46718800-46720800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:46718800-46721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:46718800-46722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:46718800-46726400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:46718800-46726600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:46718800-46727000	Weak transcription	Spleen	Spleen
27	chr2:46719400-46721400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:46719800-46721200	Enhancers	A549	lung
29	chr2:46719800-46721400	Enhancers	Fetal Heart	heart
30	chr2:46720000-46721400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:46720000-46721400	Enhancers	Hela-S3	cervix
32	chr2:46720000-46721400	Enhancers	NHLF	lung
33	chr2:46720000-46721400	Enhancers	Osteobl	bone
34	chr2:46720400-46720600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:46720400-46720600	Enhancers	Brain Anterior Caudate	brain
36	chr2:46720400-46720600	Enhancers	Placenta	Placenta
37	chr2:46720400-46720600	Enhancers	NH-A	brain
38	chr2:46720400-46720600	Enhancers	NHEK	skin
39	chr2:46720400-46720800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:46720400-46720800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr2:46720400-46720800	Enhancers	HSMM	muscle
42	chr2:46720400-46721000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:46720400-46721000	Enhancers	Colon Smooth Muscle	Colon
44	chr2:46720400-46721000	Enhancers	HUVEC	blood vessel
45	chr2:46720400-46721000	Enhancers	NHDF-Ad	bronchial
46	chr2:46720400-46721200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:46720400-46721200	Enhancers	Fetal Muscle Leg	muscle
48	chr2:46720400-46721200	Enhancers	Left Ventricle	heart
49	chr2:46720400-46721200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:46720400-46721200	Enhancers	Rectal Smooth Muscle	rectum

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