Variant report

Variant	rs1286816
Chromosome Location	chr1:62289710-62289711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62288601..62290902-chr1:62291765..62293446,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12045057	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1286813	0.82[CHB][hapmap]
rs1286815	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17371638	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2185136	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2788614	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2788616	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2799629	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2811324	0.83[ASN][1000 genomes]
rs60422848	0.80[EUR][1000 genomes]
rs7515512	1.00[JPT][hapmap]
rs7554677	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	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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62290200	Weak transcription	Lung	lung
2	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
7	chr1:62247600-62297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:62253600-62297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:62255600-62302400	Weak transcription	Brain Anterior Caudate	brain
12	chr1:62257000-62291600	Weak transcription	Gastric	stomach
13	chr1:62263400-62293200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:62263800-62303800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
16	chr1:62264200-62290200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:62264600-62292800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:62264600-62296000	Weak transcription	Fetal Brain Female	brain
19	chr1:62264600-62297400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
21	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:62265200-62293000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:62265400-62293200	Weak transcription	Fetal Stomach	stomach
24	chr1:62270800-62290200	Weak transcription	Stomach Mucosa	stomach
25	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:62272000-62290200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:62273600-62290800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:62275000-62301600	Weak transcription	Ovary	ovary
29	chr1:62275400-62293200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:62278200-62316400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:62279200-62293800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:62281200-62295200	Weak transcription	Right Ventricle	heart
33	chr1:62282400-62291600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:62282800-62303600	Weak transcription	Hela-S3	cervix
35	chr1:62283400-62296600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:62283400-62301200	Weak transcription	Brain Angular Gyrus	brain
37	chr1:62283800-62290600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:62283800-62298200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:62283800-62300400	Strong transcription	Liver	Liver
40	chr1:62283800-62302600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:62284000-62295800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:62284200-62290600	Weak transcription	Brain Germinal Matrix	brain
43	chr1:62284600-62291800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:62285000-62290800	Weak transcription	Psoas Muscle	Psoas
45	chr1:62285000-62291000	Weak transcription	Fetal Heart	heart
46	chr1:62285200-62290200	Weak transcription	NHEK	skin
47	chr1:62285200-62294600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:62285600-62294600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
50	chr1:62286200-62297800	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links