Variant report

Variant	rs2498986
Chromosome Location	chr1:62358880-62358881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10889259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889264	1.00[AFR][1000 genomes]
rs11207853	1.00[AFR][1000 genomes]
rs17252430	1.00[AMR][1000 genomes]
rs2498990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2498993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656709	1.00[AMR][1000 genomes]
rs6656711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6687261	1.00[AMR][1000 genomes]
rs6696674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7512340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7522779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7536831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7548755	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
2	chr1:62317800-62390400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:62319000-62373800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:62324400-62361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:62330400-62361000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:62331600-62371800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:62331800-62384200	Weak transcription	Gastric	stomach
8	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
9	chr1:62336200-62362400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62336400-62360200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:62336600-62380000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:62339800-62361200	Weak transcription	Lung	lung
13	chr1:62340400-62399200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:62341400-62361000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:62342600-62361000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:62344000-62362200	Weak transcription	Right Ventricle	heart
17	chr1:62344400-62367000	Weak transcription	Colonic Mucosa	Colon
18	chr1:62346000-62389400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:62348200-62360600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:62348600-62361000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:62350200-62397600	Weak transcription	Esophagus	oesophagus
23	chr1:62350400-62361000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:62350600-62360000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:62350600-62380200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:62350600-62391600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:62350800-62361200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:62350800-62363200	Weak transcription	Liver	Liver
30	chr1:62350800-62374200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:62350800-62395800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:62350800-62397800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:62350800-62417600	Weak transcription	Ovary	ovary
34	chr1:62351600-62359200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:62352200-62367000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:62352200-62375200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:62353400-62360000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:62353400-62360800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:62353400-62361000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:62353400-62378400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:62353400-62380200	Weak transcription	Aorta	Aorta
42	chr1:62353600-62396000	Weak transcription	Fetal Kidney	kidney
43	chr1:62353800-62359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:62353800-62385400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:62354200-62375200	Weak transcription	Left Ventricle	heart
47	chr1:62355200-62365200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr1:62355200-62365400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:62355800-62374800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:62357000-62360200	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links