Variant report

Variant	rs2481665
Chromosome Location	chr1:62594677-62594678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1013293	0.92[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12078747	1.00[JPT][hapmap]
rs12730782	0.83[AMR][1000 genomes]
rs17379217	0.89[MEX][hapmap];0.88[MKK][hapmap];0.84[AMR][1000 genomes]
rs1888984	1.00[JPT][hapmap]
rs1888985	1.00[JPT][hapmap]
rs2457815	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2457816	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2457817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476198	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2476201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481670	0.84[ASN][1000 genomes]
rs2481671	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2481677	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4915793	1.00[JPT][hapmap]
rs55725347	0.82[AMR][1000 genomes]
rs6661862	0.84[TSI][hapmap]
rs6668600	0.86[TSI][hapmap]
rs6670849	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs6682776	0.88[MKK][hapmap]
rs6685401	0.84[ASN][1000 genomes]
rs6703123	1.00[JPT][hapmap]
rs7514002	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555002	1.00[JPT][hapmap]
rs991007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2481665	TACSTD2	cis	cerebellum	SCAN
rs2481665	RAVER2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
6	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
7	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:62566200-62603400	Weak transcription	Esophagus	oesophagus
10	chr1:62566200-62604400	Weak transcription	Lung	lung
11	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
12	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
15	chr1:62576600-62596800	Weak transcription	Fetal Stomach	stomach
16	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
17	chr1:62576800-62607800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:62580000-62611600	Weak transcription	Pancreas	Pancrea
19	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:62584600-62603400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:62584600-62607800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:62588000-62596800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:62588600-62595000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:62588800-62602000	Weak transcription	HMEC	breast
26	chr1:62589000-62602800	Weak transcription	NHEK	skin
27	chr1:62589800-62599000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:62590200-62598400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:62590600-62594800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:62590800-62609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:62592400-62597400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:62593000-62605000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:62593200-62607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:62593400-62596200	Strong transcription	Fetal Intestine Small	intestine
36	chr1:62593400-62617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:62593600-62594800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:62593600-62596000	Strong transcription	Liver	Liver
39	chr1:62593600-62596000	Strong transcription	Fetal Intestine Large	intestine
40	chr1:62593600-62597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
42	chr1:62593800-62596200	Strong transcription	Ovary	ovary
43	chr1:62593800-62607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:62594000-62595000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:62594000-62595200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:62594200-62594800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:62594200-62595200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:62594200-62595200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:62594200-62595600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:62594200-62595800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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