Variant report

Variant	rs2666493
Chromosome Location	chr1:62614464-62614465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1811891	0.82[EUR][1000 genomes]
rs2251367	1.00[CHB][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264960	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457821	0.95[ASN][1000 genomes]
rs2457832	0.84[EUR][1000 genomes]
rs2476195	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2476196	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2476197	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476200	0.82[EUR][1000 genomes]
rs2481667	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2481668	0.90[EUR][1000 genomes]
rs2481669	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481672	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481673	0.84[EUR][1000 genomes]
rs2481674	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]
rs2481675	0.95[ASN][1000 genomes]
rs2481680	0.84[EUR][1000 genomes]
rs2481706	0.84[EUR][1000 genomes]
rs2666468	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2666491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666494	0.83[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2774932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2984823	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2989012	0.84[EUR][1000 genomes]
rs6587956	0.80[ASN][1000 genomes]
rs7520269	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530787	0.87[EUR][1000 genomes]
rs7535875	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538266	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9436220	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv822998	chr1:62613701-62616280	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2666493	ATG4C	cis	cerebellum	SCAN
rs2666493	RAVER2	cis	cerebellum	SCAN
rs2666493	FOXD3	cis	cerebellum	SCAN

Chromatin state (count:84 , 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	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
6	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:62593400-62617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
11	chr1:62594400-62614800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:62596000-62617800	Weak transcription	Aorta	Aorta
14	chr1:62599000-62616000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:62603800-62617200	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:62603800-62617400	Weak transcription	Gastric	stomach
17	chr1:62603800-62617800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:62604600-62617800	Weak transcription	Esophagus	oesophagus
19	chr1:62605000-62631800	Weak transcription	Lung	lung
20	chr1:62605200-62622400	Weak transcription	Fetal Brain Female	brain
21	chr1:62605200-62624400	Weak transcription	Right Atrium	heart
22	chr1:62606000-62617400	Weak transcription	A549	lung
23	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
24	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:62608000-62618800	Weak transcription	Brain Germinal Matrix	brain
26	chr1:62608400-62617600	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:62608400-62618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:62608600-62614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:62608600-62618400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:62608800-62627400	Weak transcription	Fetal Kidney	kidney
32	chr1:62609000-62614800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:62609000-62615200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:62609000-62620600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:62609000-62620600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:62609000-62621600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:62610400-62614600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:62610800-62616400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:62610800-62619600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:62610800-62621400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:62612000-62617800	Weak transcription	Pancreas	Pancrea
42	chr1:62612400-62629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:62612400-62632600	Weak transcription	Brain Angular Gyrus	brain
44	chr1:62612600-62616000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr1:62612600-62618200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:62612600-62625200	Weak transcription	GM12878-XiMat	blood
47	chr1:62613000-62614800	Strong transcription	Fetal Intestine Small	intestine
48	chr1:62613200-62614800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:62613200-62619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links