Variant report

Variant	rs62158019
Chromosome Location	chr2:99316339-99316340
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	chr2:99299792..99302673-chr2:99315201..99317831,2	MCF-7	breast:
2	chr2:99316162..99318899-chr2:99339583..99342162,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10172913	0.83[EUR][1000 genomes]
rs10496329	0.83[EUR][1000 genomes]
rs12464653	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12467276	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12468086	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12469616	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2871235	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56363239	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62158012	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62158020	0.84[EUR][1000 genomes]
rs62158022	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742760	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs882164	0.87[AMR][1000 genomes];0.87[EUR][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	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
2	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:99294400-99318600	Weak transcription	Spleen	Spleen
4	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:99302400-99318400	Weak transcription	Ovary	ovary
6	chr2:99303200-99336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:99304000-99318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:99305000-99316800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:99308000-99317800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:99309800-99318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:99310000-99317800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:99310800-99318000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:99310800-99318400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:99310800-99318400	Weak transcription	Fetal Thymus	thymus
15	chr2:99310800-99320200	Weak transcription	Thymus	Thymus
16	chr2:99311400-99320800	Weak transcription	Dnd41	blood
17	chr2:99312200-99317600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:99312200-99317600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:99312600-99317600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:99312800-99316400	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:99312800-99317000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr2:99313000-99318400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:99313000-99327000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:99313200-99318200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:99313200-99326600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:99313800-99316800	Enhancers	Small Intestine	intestine
27	chr2:99313800-99317600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:99314000-99317600	Weak transcription	Brain Angular Gyrus	brain
29	chr2:99314000-99317800	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:99314200-99317600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:99314200-99317600	Weak transcription	Fetal Kidney	kidney
32	chr2:99314200-99322000	Enhancers	Fetal Intestine Small	intestine
33	chr2:99314400-99317400	Enhancers	Left Ventricle	heart
34	chr2:99314400-99317800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:99314400-99318600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:99314800-99317600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:99315000-99316400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:99315000-99316400	Enhancers	Pancreas	Pancrea
39	chr2:99315000-99316600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr2:99315000-99316800	Genic enhancers	Primary T cells from cord blood	blood
41	chr2:99315000-99316800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:99315000-99322200	Enhancers	Fetal Intestine Large	intestine
43	chr2:99315200-99316600	Strong transcription	HepG2	liver
44	chr2:99315200-99318000	Weak transcription	Brain Anterior Caudate	brain
45	chr2:99315400-99316600	Genic enhancers	Lung	lung
46	chr2:99315400-99317400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:99315400-99319000	Enhancers	HUVEC	blood vessel
48	chr2:99315400-99319400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:99315600-99316600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:99315600-99316600	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links