Variant report

Variant	rs4973289
Chromosome Location	chr2:231049142-231049143
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231042254..231045167-chr2:231047833..231049865,3	K562	blood:

Variant related genes	Relation type
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10168052	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10755048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755050	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124534	0.81[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12474611	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12474616	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615975	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12616762	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618921	0.98[ASN][1000 genomes]
rs12619729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469345	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1896258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1896259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1978583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985603	0.93[ASN][1000 genomes]
rs2081714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114592	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2396709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396711	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769837	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769839	0.86[ASN][1000 genomes]
rs3948464	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs41309108	0.93[ASN][1000 genomes]
rs41345344	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41423848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4327229	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972942	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973286	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973290	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4973291	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4973292	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973293	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973296	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4973297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55809057	0.93[ASN][1000 genomes]
rs55945652	0.95[ASN][1000 genomes]
rs55956818	0.88[ASN][1000 genomes]
rs56159955	0.93[ASN][1000 genomes]
rs56275915	0.92[ASN][1000 genomes]
rs56301614	0.98[ASN][1000 genomes]
rs56412815	0.92[ASN][1000 genomes]
rs59536070	0.93[ASN][1000 genomes]
rs61182521	0.93[ASN][1000 genomes]
rs6436919	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6735604	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6736220	0.80[EUR][1000 genomes]
rs6743028	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67469122	0.93[ASN][1000 genomes]
rs6750748	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6752361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6755998	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72982403	0.93[ASN][1000 genomes]
rs72982411	0.93[ASN][1000 genomes]
rs72982413	0.84[ASN][1000 genomes]
rs72982416	0.93[ASN][1000 genomes]
rs72982421	0.93[ASN][1000 genomes]
rs72982424	0.86[ASN][1000 genomes]
rs73000348	0.95[ASN][1000 genomes]
rs73000367	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73000371	0.93[ASN][1000 genomes]
rs7561924	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7583769	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592927	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601190	0.83[EUR][1000 genomes]
rs7601299	0.83[EUR][1000 genomes]
rs7603350	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930031	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats 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	4 gene(s)	inside rSNPs	diseases
6	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231028400-231067000	Strong transcription	Primary B cells from peripheral blood	blood
2	chr2:231028600-231051200	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:231028800-231051600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:231030800-231051000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:231030800-231051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:231031200-231049800	Weak transcription	HSMMtube	muscle
7	chr2:231031400-231051000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:231031400-231051000	Strong transcription	Fetal Thymus	thymus
9	chr2:231031400-231051600	Strong transcription	GM12878-XiMat	blood
10	chr2:231031400-231061200	Strong transcription	Primary B cells from cord blood	blood
11	chr2:231031600-231050800	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:231031600-231052400	Weak transcription	Fetal Brain Male	brain
13	chr2:231031800-231049400	Strong transcription	Liver	Liver
14	chr2:231033800-231050800	Strong transcription	Dnd41	blood
15	chr2:231035000-231051800	Strong transcription	Primary T cells from cord blood	blood
16	chr2:231035400-231077000	Weak transcription	HepG2	liver
17	chr2:231035600-231050400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:231035600-231050400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:231035600-231050800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:231035600-231050800	Strong transcription	Thymus	Thymus
21	chr2:231035600-231051000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:231035600-231051000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:231035600-231051200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:231035600-231051600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:231035800-231049600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:231035800-231062800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:231036200-231049200	Strong transcription	Adipose Nuclei	Adipose
28	chr2:231036200-231050800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:231036200-231051200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:231036400-231051200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:231036600-231051200	Strong transcription	Ovary	ovary
32	chr2:231036800-231051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:231036800-231071800	Weak transcription	NHEK	skin
34	chr2:231036800-231073600	Weak transcription	HMEC	breast
35	chr2:231037200-231050800	Strong transcription	Spleen	Spleen
36	chr2:231037200-231051000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:231037400-231049800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:231038000-231069600	Weak transcription	NHLF	lung
39	chr2:231038800-231049200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:231039000-231050800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:231039000-231050800	Strong transcription	Fetal Stomach	stomach
42	chr2:231039400-231050000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:231041400-231064600	Weak transcription	Osteobl	bone
44	chr2:231041800-231049200	Strong transcription	Aorta	Aorta
45	chr2:231042800-231058400	Weak transcription	Brain Anterior Caudate	brain
46	chr2:231042800-231062600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:231043000-231062800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:231043800-231049200	Strong transcription	Esophagus	oesophagus
49	chr2:231043800-231057800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:231043800-231062600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links