Variant report

Variant	rs2346412
Chromosome Location	chr2:46718989-46718990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46713674..46717376-chr2:46717590..46719594,3	K562	blood:
2	chr2:46707494..46710484-chr2:46718946..46721502,2	K562	blood:
3	chr2:46713674..46716471-chr2:46717649..46719594,2	K562	blood:
4	chr2:46715260..46716783-chr2:46718663..46721578,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11682326	0.81[EUR][1000 genomes]
rs6713990	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758999	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609080	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv581746	chr2:46699145-46719922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv581747	chr2:46709571-46718989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	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
17	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2346412	OXER1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46714600-46719200	Enhancers	Left Ventricle	heart
2	chr2:46714800-46720800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:46715400-46720400	Weak transcription	HUVEC	blood vessel
5	chr2:46715800-46719800	Weak transcription	A549	lung
6	chr2:46715800-46720400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:46716200-46719000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:46716400-46719000	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:46716600-46720400	Enhancers	GM12878-XiMat	blood
10	chr2:46717200-46720000	Weak transcription	Osteobl	bone
11	chr2:46717600-46720000	Weak transcription	Hela-S3	cervix
12	chr2:46717800-46720400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:46718000-46720400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:46718000-46722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:46718200-46720400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:46718200-46720400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:46718200-46720400	Weak transcription	Fetal Brain Female	brain
18	chr2:46718200-46720400	Weak transcription	Placenta	Placenta
19	chr2:46718200-46720400	Weak transcription	HSMM	muscle
20	chr2:46718200-46720400	Weak transcription	NH-A	brain
21	chr2:46718200-46720600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:46718200-46720800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:46718200-46721000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:46718200-46722600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:46718200-46726600	Weak transcription	Aorta	Aorta
26	chr2:46718400-46719000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:46718400-46719400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:46718400-46719600	Bivalent Enhancer	HepG2	liver
29	chr2:46718400-46720400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:46718400-46720400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:46718400-46720400	Weak transcription	HSMMtube	muscle
32	chr2:46718400-46720400	Weak transcription	NHDF-Ad	bronchial
33	chr2:46718400-46720600	Weak transcription	Ovary	ovary
34	chr2:46718400-46721000	Enhancers	Brain Hippocampus Middle	brain
35	chr2:46718400-46721000	Weak transcription	Right Atrium	heart
36	chr2:46718400-46726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:46718600-46720600	Weak transcription	Brain Germinal Matrix	brain
38	chr2:46718600-46720600	Weak transcription	Fetal Brain Male	brain
39	chr2:46718600-46722000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:46718600-46722600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:46718600-46725600	Weak transcription	Brain Substantia Nigra	brain
42	chr2:46718600-46726600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:46718600-46726600	Weak transcription	Right Ventricle	heart
44	chr2:46718800-46719800	Weak transcription	Fetal Heart	heart
45	chr2:46718800-46720000	Weak transcription	NHLF	lung
46	chr2:46718800-46720400	Weak transcription	Brain Anterior Caudate	brain
47	chr2:46718800-46720400	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:46718800-46720400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:46718800-46720800	Weak transcription	Fetal Stomach	stomach
50	chr2:46718800-46720800	Weak transcription	Stomach Smooth Muscle	stomach

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