Variant report

Variant	rs12408315
Chromosome Location	chr1:62300862-62300863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62294253..62296248-chr1:62299623..62302341,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12402847	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408105	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410306	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728331	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749061	0.81[AMR][1000 genomes]
rs1286815	0.98[EUR][1000 genomes]
rs2938	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34403905	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473594	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35180388	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35318456	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35722784	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61770106	1.00[ASN][1000 genomes]
rs71641748	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1099	chr1:62275317-62315943	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
3	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:62255600-62302400	Weak transcription	Brain Anterior Caudate	brain
6	chr1:62263800-62303800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
8	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
9	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:62275000-62301600	Weak transcription	Ovary	ovary
12	chr1:62278200-62316400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:62282800-62303600	Weak transcription	Hela-S3	cervix
14	chr1:62283400-62301200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:62283800-62302600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
17	chr1:62287600-62301600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:62287800-62302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:62289400-62305400	Weak transcription	A549	lung
20	chr1:62290000-62304600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:62290600-62308600	Weak transcription	Brain Substantia Nigra	brain
22	chr1:62290800-62326000	Weak transcription	Left Ventricle	heart
23	chr1:62291400-62305000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:62291600-62305000	Weak transcription	Fetal Heart	heart
25	chr1:62292000-62301000	Weak transcription	Psoas Muscle	Psoas
26	chr1:62292000-62304800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:62292000-62309200	Weak transcription	Gastric	stomach
28	chr1:62292200-62302200	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:62292400-62302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:62293400-62302000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:62293600-62302200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:62293800-62321600	Weak transcription	Esophagus	oesophagus
33	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:62294400-62304000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:62294400-62330200	Weak transcription	Fetal Stomach	stomach
36	chr1:62294600-62321000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:62294800-62301000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:62294800-62302000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:62294800-62305200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:62294800-62324000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:62295000-62322600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:62295200-62304600	Weak transcription	NHEK	skin
43	chr1:62295200-62307600	Weak transcription	Aorta	Aorta
44	chr1:62295800-62302400	Weak transcription	HepG2	liver
45	chr1:62295800-62310800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:62295800-62321600	Weak transcription	Primary T cells from cord blood	blood
47	chr1:62296000-62302200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:62296000-62303000	Weak transcription	HMEC	breast
49	chr1:62296000-62303200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:62296000-62304000	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links