Variant report

Variant	rs56945529
Chromosome Location	chr2:99311400-99311401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10165386	0.83[EUR][1000 genomes]
rs10199926	0.81[EUR][1000 genomes]
rs17448085	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17448190	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448211	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17448420	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17514013	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309434	0.87[EUR][1000 genomes]
rs3769688	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55633363	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55634708	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55646762	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55730719	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55859362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55939630	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56027617	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56070038	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56163086	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56305624	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354279	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56371690	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375699	0.86[EUR][1000 genomes]
rs60889948	0.87[EUR][1000 genomes]
rs62157995	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62157997	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62157999	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158000	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158001	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158002	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158008	0.87[EUR][1000 genomes]
rs62158009	0.86[EUR][1000 genomes]
rs62158010	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62158012	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62158015	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6742636	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72825754	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
2	chr2:99292200-99312800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:99294200-99313600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:99294200-99315000	Weak transcription	Fetal Intestine Large	intestine
6	chr2:99294400-99315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:99294400-99318600	Weak transcription	Spleen	Spleen
8	chr2:99294600-99312600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:99294600-99314200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:99295200-99312600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:99300000-99315600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:99301600-99315800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:99302400-99318400	Weak transcription	Ovary	ovary
15	chr2:99302600-99313000	Weak transcription	Right Ventricle	heart
16	chr2:99303200-99336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:99303800-99311800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:99304000-99318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:99305000-99316800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:99307000-99315600	Weak transcription	Colonic Mucosa	Colon
21	chr2:99307200-99311400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:99308000-99311800	Weak transcription	Gastric	stomach
23	chr2:99308000-99312000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:99308000-99312600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:99308000-99315600	Weak transcription	Right Atrium	heart
26	chr2:99308000-99317800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:99308200-99311400	Enhancers	Primary T cells from cord blood	blood
28	chr2:99308200-99312800	Weak transcription	Brain Substantia Nigra	brain
29	chr2:99308400-99311600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:99308400-99311600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:99308400-99311800	Weak transcription	Left Ventricle	heart
32	chr2:99308400-99312800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:99308400-99312800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:99308400-99313000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:99308400-99313600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:99308800-99311600	Weak transcription	Pancreas	Pancrea
37	chr2:99309600-99311800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:99309600-99315000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:99309800-99318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:99310000-99313000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr2:99310000-99317800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr2:99310200-99311800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:99310400-99311400	Enhancers	Dnd41	blood
44	chr2:99310600-99315400	Weak transcription	HUVEC	blood vessel
45	chr2:99310800-99311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:99310800-99313400	Weak transcription	HepG2	liver
47	chr2:99310800-99315400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:99310800-99315400	Weak transcription	Lung	lung
49	chr2:99310800-99318000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:99310800-99318400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links