Variant report

Variant	rs1530621
Chromosome Location	chr2:46688688-46688689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46593545..46595636-chr2:46687242..46688788,2	MCF-7	breast:
2	chr2:46673194..46677108-chr2:46685172..46689084,4	MCF-7	breast:
3	chr2:46561048..46561822-chr2:46688208..46689083,4	MCF-7	breast:
4	chr1:116681465..116682280-chr2:46688520..46689243,2	MCF-7	breast:
5	chr2:46591734..46592648-chr2:46688138..46688776,3	MCF-7	breast:
6	chr2:46236576..46237543-chr2:46688264..46688946,2	K562	blood:
7	chr2:46219810..46222412-chr2:46687121..46689791,4	MCF-7	breast:
8	chr2:46616166..46617034-chr2:46688295..46689079,2	MCF-7	breast:
9	chr2:46219968..46221252-chr2:46688230..46688933,7	MCF-7	breast:
10	chr2:46688652..46689180-chr2:46781896..46782657,2	K562	blood:
11	chr2:46237659..46238661-chr2:46688156..46689453,6	K562	blood:
12	chr2:46630338..46632777-chr2:46688493..46691339,2	K562	blood:
13	chr2:46305890..46306846-chr2:46688252..46689134,2	K562	blood:
14	chr2:46679860..46680421-chr2:46688244..46689196,2	K562	blood:
15	chr2:46593115..46594090-chr2:46688546..46689223,4	MCF-7	breast:
16	chr2:46237923..46238577-chr2:46688234..46688787,2	MCF-7	breast:
17	chr2:46289850..46290391-chr2:46688641..46689585,2	K562	blood:
18	chr2:46290043..46290623-chr2:46688446..46689207,2	MCF-7	breast:
19	chr2:46593059..46594102-chr2:46688159..46689154,5	MCF-7	breast:
20	chr2:46456901..46457866-chr2:46688300..46689178,2	MCF-7	breast:
21	chr2:46636115..46638908-chr2:46687157..46689113,2	MCF-7	breast:
22	chr2:46220268..46221206-chr2:46687774..46688837,4	K562	blood:
23	chr2:46672833..46675155-chr2:46688573..46690823,2	K562	blood:
24	chr2:46688671..46689364-chr2:46877354..46878282,2	K562	blood:
25	chr2:46561139..46561747-chr2:46688216..46688974,2	MCF-7	breast:
26	chr2:46237778..46238646-chr2:46688238..46688812,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232696	Chromatin interaction
ENSG00000241791	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11125075	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs12986653	0.91[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs12986899	0.91[EUR][1000 genomes]
rs13002880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13003074	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13007688	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs13011481	1.00[YRI][hapmap]
rs13011721	1.00[JPT][hapmap]
rs13020043	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13024414	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13030579	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs1530624	0.85[EUR][1000 genomes]
rs1530628	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs1597040	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1900591	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2121698	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2121700	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34854267	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35509718	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36006825	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754556	0.82[YRI][hapmap]
rs3768730	1.00[YRI][hapmap]
rs4312543	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4396767	0.84[EUR][1000 genomes]
rs4549147	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4563285	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4952830	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4952831	0.82[YRI][hapmap]
rs4952833	0.82[YRI][hapmap]
rs4953365	0.82[AFR][1000 genomes]
rs4953372	0.81[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4953379	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4953387	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4953388	0.87[ASW][hapmap];0.91[CEU][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4953390	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6544895	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544898	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap]
rs6718875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749877	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757564	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs718849	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556828	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7557190	0.82[YRI][hapmap]
rs7565188	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7565770	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs7607633	0.82[YRI][hapmap]
rs880671	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1530621	CRIPT	cis	lymphoblastoid	seeQTL
rs1530621	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs1530621	CRIPT	cis	parietal	SCAN
rs1530621	RHOQ	cis	cerebellum	SCAN
rs1530621	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs1530621	ATP6V1E2	cis	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46686000-46689000	Enhancers	Adipose Nuclei	Adipose
2	chr2:46686200-46688800	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:46686400-46689000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:46686400-46689000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:46686400-46689000	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr2:46686400-46689200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:46686400-46689200	Enhancers	Right Atrium	heart
8	chr2:46686400-46689400	Enhancers	Lung	lung
9	chr2:46686400-46704400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:46686600-46689000	Enhancers	Duodenum Mucosa	Duodenum
11	chr2:46686600-46689000	Enhancers	NHLF	lung
12	chr2:46686800-46691600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:46687000-46689000	Enhancers	Pancreas	Pancrea
14	chr2:46687000-46689200	Enhancers	Hela-S3	cervix
15	chr2:46687200-46689000	Enhancers	Stomach Mucosa	stomach
16	chr2:46687200-46689200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:46687200-46690600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:46687400-46689000	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr2:46687400-46689000	Enhancers	Ovary	ovary
20	chr2:46687400-46689200	Enhancers	Placenta	Placenta
21	chr2:46687600-46688800	Flanking Active TSS	HepG2	liver
22	chr2:46687600-46691600	Enhancers	NHDF-Ad	bronchial
23	chr2:46687600-46691800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:46687800-46688800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:46687800-46689200	Enhancers	A549	lung
26	chr2:46687800-46691800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:46688000-46688800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:46688000-46689000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:46688000-46689000	Enhancers	K562	blood
30	chr2:46688000-46689200	Enhancers	Fetal Thymus	thymus
31	chr2:46688200-46688800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:46688200-46688800	Enhancers	GM12878-XiMat	blood
33	chr2:46688200-46689000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:46688200-46691600	Weak transcription	Fetal Brain Male	brain
35	chr2:46688400-46688800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:46688400-46688800	Enhancers	Primary B cells from cord blood	blood
37	chr2:46688400-46688800	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:46688400-46688800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:46688400-46688800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:46688400-46688800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr2:46688400-46688800	Enhancers	Dnd41	blood
42	chr2:46688400-46689000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:46688400-46689000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:46688400-46689000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:46688400-46689000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:46688400-46689000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:46688400-46689200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:46688400-46689200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr2:46688400-46689400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:46688400-46689400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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