Variant report

Variant	rs2481674
Chromosome Location	chr1:62617623-62617624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2251367	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2264960	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457821	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457832	0.90[EUR][1000 genomes]
rs2476195	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2476196	0.87[EUR][1000 genomes]
rs2476197	0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2481667	0.84[EUR][1000 genomes]
rs2481668	0.83[EUR][1000 genomes]
rs2481669	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2481672	0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481675	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481680	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2481706	0.90[EUR][1000 genomes]
rs2666468	0.89[EUR][1000 genomes]
rs2666491	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2666493	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2666494	0.82[TSI][hapmap]
rs2774932	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2984823	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989012	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587956	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7520269	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7530787	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7535875	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7538266	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2481674	INADL	cis	cerebellum	SCAN
rs2481674	RAVER2	cis	cerebellum	SCAN
rs2481674	ATG4C	cis	cerebellum	SCAN

Chromatin state (count:77 , 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	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
5	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
8	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:62596000-62617800	Weak transcription	Aorta	Aorta
10	chr1:62603800-62617800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:62604600-62617800	Weak transcription	Esophagus	oesophagus
12	chr1:62605000-62631800	Weak transcription	Lung	lung
13	chr1:62605200-62622400	Weak transcription	Fetal Brain Female	brain
14	chr1:62605200-62624400	Weak transcription	Right Atrium	heart
15	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
16	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:62608000-62618800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:62608400-62618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:62608600-62618400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:62608800-62627400	Weak transcription	Fetal Kidney	kidney
22	chr1:62609000-62620600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:62609000-62620600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:62609000-62621600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:62610800-62619600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:62610800-62621400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:62612000-62617800	Weak transcription	Pancreas	Pancrea
28	chr1:62612400-62629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:62612400-62632600	Weak transcription	Brain Angular Gyrus	brain
30	chr1:62612600-62618200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr1:62612600-62625200	Weak transcription	GM12878-XiMat	blood
32	chr1:62613200-62619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:62613800-62618000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:62613800-62621200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:62614000-62618000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:62614000-62618200	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:62614000-62618200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:62614000-62619200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:62614000-62619600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:62614000-62621200	Strong transcription	Fetal Intestine Large	intestine
42	chr1:62614000-62621400	Strong transcription	Liver	Liver
43	chr1:62614200-62618600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:62614400-62628400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:62614400-62628800	Weak transcription	Ovary	ovary
46	chr1:62614600-62619400	Weak transcription	Adipose Nuclei	Adipose
47	chr1:62614600-62620600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:62614600-62620800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:62615200-62629000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:62615200-62629400	Weak transcription	NHEK	skin

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