Variant report

Variant	rs2008275
Chromosome Location	chr20:24964202-24964203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24959468..24961705-chr20:24961994..24965467,4	K562	blood:
2	chr20:24962863..24965787-chr20:24971009..24974027,3	K562	blood:
3	chr20:24963189..24966768-chr20:24970100..24973416,3	MCF-7	breast:
4	chr20:24963187..24967390-chr20:24970058..24973702,4	K562	blood:
5	chr20:24962499..24965944-chr20:24971624..24973670,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056036	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11087486	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11699285	0.81[EUR][1000 genomes]
rs11700073	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11905625	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11906373	0.88[ASN][1000 genomes]
rs12625319	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13041643	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535042	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2092565	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2103736	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2151462	0.88[ASN][1000 genomes]
rs2151463	0.88[ASN][1000 genomes]
rs2179729	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179730	0.93[ASN][1000 genomes]
rs2179732	1.00[JPT][hapmap]
rs2206891	0.87[ASN][1000 genomes]
rs2225459	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235847	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227613	0.84[ASN][1000 genomes]
rs227614	0.86[ASN][1000 genomes]
rs227615	0.82[ASN][1000 genomes]
rs227616	0.88[ASN][1000 genomes]
rs227618	0.81[ASN][1000 genomes]
rs227619	0.86[ASN][1000 genomes]
rs227620	0.86[ASN][1000 genomes]
rs227621	0.88[ASN][1000 genomes]
rs227622	0.88[ASN][1000 genomes]
rs227623	0.86[ASN][1000 genomes]
rs227624	0.88[ASN][1000 genomes]
rs227625	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs227626	0.86[ASN][1000 genomes]
rs227627	0.86[ASN][1000 genomes]
rs227628	0.86[ASN][1000 genomes]
rs227629	0.88[ASN][1000 genomes]
rs227630	0.88[ASN][1000 genomes]
rs227631	0.88[ASN][1000 genomes]
rs227632	0.88[ASN][1000 genomes]
rs227633	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227634	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227635	0.86[ASN][1000 genomes]
rs227639	0.86[ASN][1000 genomes]
rs227643	0.86[ASN][1000 genomes]
rs227646	0.86[ASN][1000 genomes]
rs227648	0.86[ASN][1000 genomes]
rs227650	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227651	0.88[ASN][1000 genomes]
rs227652	0.86[ASN][1000 genomes]
rs227653	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227657	0.86[ASN][1000 genomes]
rs227658	0.88[ASN][1000 genomes]
rs227659	0.86[ASN][1000 genomes]
rs2387366	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2387572	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424691	0.88[ASN][1000 genomes]
rs2892279	0.93[ASN][1000 genomes]
rs34419834	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3746330	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4527284	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4539860	0.81[ASN][1000 genomes]
rs45468392	0.86[ASN][1000 genomes]
rs45556041	0.86[ASN][1000 genomes]
rs4594518	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4813541	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813542	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815337	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815339	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815340	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815341	0.93[ASN][1000 genomes]
rs4815351	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4815355	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815357	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56312312	0.93[ASN][1000 genomes]
rs57265446	0.88[ASN][1000 genomes]
rs58244398	0.91[ASN][1000 genomes]
rs6050177	0.93[ASN][1000 genomes]
rs6050179	0.93[ASN][1000 genomes]
rs6050181	0.93[ASN][1000 genomes]
rs6050198	1.00[CHB][hapmap]
rs6050201	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6050249	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6050255	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050259	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050261	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6083684	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083685	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083686	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083688	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083692	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083699	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106975	0.93[ASN][1000 genomes]
rs6106984	0.93[ASN][1000 genomes]
rs6114980	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114981	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114984	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114988	0.93[ASN][1000 genomes]
rs6114992	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6132773	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132774	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132775	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132777	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132778	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132783	0.84[ASN][1000 genomes]
rs6132784	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6132789	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138406	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138417	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138423	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138425	0.81[AFR][1000 genomes]
rs6138426	0.84[AFR][1000 genomes]
rs6138431	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138435	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138437	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138438	0.86[ASN][1000 genomes]
rs6138442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138455	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138456	0.91[ASN][1000 genomes]
rs6138457	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138458	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6138460	0.84[ASN][1000 genomes]
rs6138461	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138473	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs62215110	0.86[ASN][1000 genomes]
rs62215115	0.86[ASN][1000 genomes]
rs62215128	0.91[ASN][1000 genomes]
rs62215131	0.91[ASN][1000 genomes]
rs6707	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7268095	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7269416	0.93[ASN][1000 genomes]
rs735886	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8125909	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8183891	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926661	0.93[ASN][1000 genomes]
rs926662	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008275	C20orf3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24935200-24971800	Weak transcription	K562	blood
2	chr20:24942000-24972400	Weak transcription	Fetal Heart	heart
3	chr20:24943200-24965000	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr20:24950000-24966400	Weak transcription	Small Intestine	intestine
5	chr20:24953600-24972000	Weak transcription	NH-A	brain
6	chr20:24954200-24965800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr20:24954800-24965800	Weak transcription	Psoas Muscle	Psoas
8	chr20:24957200-24964600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr20:24957600-24965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr20:24957800-24966000	Strong transcription	Primary T cells from cord blood	blood
11	chr20:24957800-24972000	Weak transcription	HUVEC	blood vessel
12	chr20:24958000-24965600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:24958000-24970400	Weak transcription	Fetal Brain Male	brain
14	chr20:24958000-24971800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:24958000-24972200	Weak transcription	Fetal Kidney	kidney
16	chr20:24958200-24965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr20:24960000-24965000	Weak transcription	Right Atrium	heart
18	chr20:24960400-24964600	Strong transcription	Fetal Muscle Leg	muscle
19	chr20:24960600-24964400	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr20:24960600-24964600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:24960800-24971800	Weak transcription	Stomach Mucosa	stomach
22	chr20:24961000-24964400	Strong transcription	HepG2	liver
23	chr20:24961200-24964600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr20:24961200-24964600	Strong transcription	Brain Anterior Caudate	brain
25	chr20:24961200-24964800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr20:24961400-24964600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:24961400-24964600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr20:24961400-24964800	Strong transcription	Fetal Stomach	stomach
29	chr20:24961400-24965000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr20:24961400-24965200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr20:24961400-24971800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr20:24961600-24964400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr20:24961600-24964400	Strong transcription	Placenta	Placenta
34	chr20:24961600-24964600	Strong transcription	Thymus	Thymus
35	chr20:24961600-24964800	Strong transcription	Fetal Intestine Large	intestine
36	chr20:24961600-24965000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:24961600-24965200	Strong transcription	Dnd41	blood
38	chr20:24961600-24971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr20:24961600-24971800	Weak transcription	NHLF	lung
40	chr20:24961600-24972600	Weak transcription	Aorta	Aorta
41	chr20:24961800-24964600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr20:24961800-24971400	Weak transcription	HMEC	breast
43	chr20:24962000-24964400	Strong transcription	Brain Hippocampus Middle	brain
44	chr20:24962000-24964600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr20:24962000-24964800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr20:24962000-24964800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr20:24962000-24969400	Weak transcription	NHEK	skin
48	chr20:24962000-24971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr20:24962000-24971800	Weak transcription	Pancreas	Pancrea
50	chr20:24962200-24966400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links