Variant report

Variant	rs7268095
Chromosome Location	chr20:24972333-24972334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24972188..24974753-chr20:24992355..24994002,2	K562	blood:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:24972013..24974485-chr20:25388171..25390084,2	MCF-7	breast:
4	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
5	chr20:24972059..24974449-chr20:25176101..25177683,2	MCF-7	breast:
6	chr20:24971946..24973582-chr20:25227704..25229248,2	MCF-7	breast:
7	chr20:24971839..24974533-chr20:25228512..25230139,2	MCF-7	breast:
8	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101003	Chromatin interaction
ENSG00000100987	Chromatin interaction
ENSG00000154930	Chromatin interaction
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.88[ASN][1000 genomes]
rs1056036	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11700073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11905625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906373	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12625319	0.86[ASN][1000 genomes]
rs13041643	0.88[ASN][1000 genomes]
rs1331286	0.83[ASN][1000 genomes]
rs1535042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1854849	0.83[ASN][1000 genomes]
rs1977540	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2092565	0.88[ASN][1000 genomes]
rs2103736	0.88[ASN][1000 genomes]
rs2151462	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2151463	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179729	0.88[ASN][1000 genomes]
rs2179730	0.86[ASN][1000 genomes]
rs2179732	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2225459	0.88[ASN][1000 genomes]
rs2235847	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs227590	0.85[ASN][1000 genomes]
rs227597	0.83[ASN][1000 genomes]
rs227598	0.80[ASN][1000 genomes]
rs227613	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227614	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227615	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227616	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227618	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227619	0.93[ASN][1000 genomes]
rs227620	0.93[ASN][1000 genomes]
rs227621	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227622	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227623	0.93[ASN][1000 genomes]
rs227624	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227626	0.93[ASN][1000 genomes]
rs227627	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227628	0.93[ASN][1000 genomes]
rs227629	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227630	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227631	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227632	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227634	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227635	0.93[ASN][1000 genomes]
rs227639	0.93[ASN][1000 genomes]
rs227643	0.93[ASN][1000 genomes]
rs227646	0.93[ASN][1000 genomes]
rs227648	0.93[ASN][1000 genomes]
rs227649	0.83[ASN][1000 genomes]
rs227650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227651	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227652	0.93[ASN][1000 genomes]
rs227653	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227657	0.93[ASN][1000 genomes]
rs227658	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227659	0.93[ASN][1000 genomes]
rs2387365	0.83[ASN][1000 genomes]
rs2387366	0.88[ASN][1000 genomes]
rs2387572	0.88[ASN][1000 genomes]
rs2424691	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2892279	0.86[ASN][1000 genomes]
rs34419834	0.88[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4273288	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4527284	0.82[ASN][1000 genomes]
rs4539860	0.88[ASN][1000 genomes]
rs45468392	0.93[ASN][1000 genomes]
rs45556041	0.93[ASN][1000 genomes]
rs4813541	0.88[ASN][1000 genomes]
rs4813542	0.88[ASN][1000 genomes]
rs4815325	0.80[EUR][1000 genomes]
rs4815327	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815337	0.88[ASN][1000 genomes]
rs4815339	0.86[ASN][1000 genomes]
rs4815340	0.88[ASN][1000 genomes]
rs4815341	0.86[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4815355	0.88[ASN][1000 genomes]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs56312312	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57265446	0.95[ASN][1000 genomes]
rs58244398	0.97[ASN][1000 genomes]
rs6036976	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050134	0.83[ASN][1000 genomes]
rs6050177	0.86[ASN][1000 genomes]
rs6050179	0.86[ASN][1000 genomes]
rs6050181	0.86[ASN][1000 genomes]
rs6050198	0.85[CHB][hapmap]
rs6050201	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050249	0.82[CHB][hapmap];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	0.88[ASN][1000 genomes]
rs6083685	0.88[ASN][1000 genomes]
rs6083686	0.88[ASN][1000 genomes]
rs6083688	0.88[ASN][1000 genomes]
rs6083692	0.86[ASN][1000 genomes]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6106975	0.86[ASN][1000 genomes]
rs6106984	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs6114984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114988	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114992	0.82[ASN][1000 genomes]
rs6132773	0.88[ASN][1000 genomes]
rs6132774	0.88[ASN][1000 genomes]
rs6132775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132783	0.90[ASN][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6132785	0.81[ASN][1000 genomes]
rs6132789	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138417	0.88[ASN][1000 genomes]
rs6138423	0.88[ASN][1000 genomes]
rs6138431	0.82[ASN][1000 genomes]
rs6138435	0.88[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6138438	0.93[ASN][1000 genomes]
rs6138442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6138455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138456	0.97[ASN][1000 genomes]
rs6138457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138460	0.90[ASN][1000 genomes]
rs6138461	0.87[ASN][1000 genomes]
rs6138463	0.85[ASN][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6138473	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs62215110	0.93[ASN][1000 genomes]
rs62215115	0.93[ASN][1000 genomes]
rs62215128	0.97[ASN][1000 genomes]
rs62215131	0.97[ASN][1000 genomes]
rs6707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7269416	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735886	0.88[ASN][1000 genomes]
rs8125909	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs914314	0.83[ASN][1000 genomes]
rs926661	0.86[ASN][1000 genomes]
rs926662	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7268095	PYGB	cis	parietal	SCAN
rs7268095	CST9	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24942000-24972400	Weak transcription	Fetal Heart	heart
2	chr20:24961600-24972600	Weak transcription	Aorta	Aorta
3	chr20:24962200-24972600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:24962800-24972600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:24962800-24972600	Weak transcription	Ovary	ovary
6	chr20:24963200-24972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:24964000-24972400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:24964600-24972400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:24968400-24972600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:24970200-24972400	Weak transcription	Fetal Intestine Large	intestine
11	chr20:24970600-24972400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr20:24971000-24972400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr20:24971000-24972600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr20:24971000-24972800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr20:24971000-24972800	Flanking Active TSS	Dnd41	blood
16	chr20:24971000-24973200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr20:24971000-24974200	Active TSS	Right Atrium	heart
18	chr20:24971200-24972400	Active TSS	Primary hematopoietic stem cells	blood
19	chr20:24971200-24972400	Enhancers	HSMM	muscle
20	chr20:24971200-24973600	Active TSS	Liver	Liver
21	chr20:24971400-24972400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr20:24971400-24972400	Flanking Active TSS	HepG2	liver
23	chr20:24971400-24972400	Flanking Active TSS	NHEK	skin
24	chr20:24971400-24972800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr20:24971400-24973000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr20:24971600-24972400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:24971600-24972400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr20:24971600-24972400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:24971600-24972400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr20:24971600-24972400	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr20:24971600-24972400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr20:24971600-24972400	Enhancers	Fetal Muscle Leg	muscle
33	chr20:24971600-24972400	Enhancers	Fetal Thymus	thymus
34	chr20:24971600-24972400	Enhancers	Lung	lung
35	chr20:24971600-24972400	Enhancers	Psoas Muscle	Psoas
36	chr20:24971600-24972400	Flanking Active TSS	GM12878-XiMat	blood
37	chr20:24971600-24972600	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr20:24971600-24972600	Enhancers	Left Ventricle	heart
39	chr20:24971600-24972600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr20:24971600-24972600	Enhancers	Small Intestine	intestine
41	chr20:24971600-24972800	Flanking Active TSS	Hela-S3	cervix
42	chr20:24971600-24973000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr20:24971600-24973200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr20:24971600-24973200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr20:24971600-24973200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr20:24971800-24972400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr20:24971800-24972400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:24971800-24972400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:24971800-24972400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr20:24971800-24972400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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