Variant report

Variant	rs6050249
Chromosome Location	chr20:24994289-24994290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24993232..24996113-chr20:25036389..25038769,2	MCF-7	breast:
2	chr20:24994027..24995709-chr20:25038377..25040983,2	MCF-7	breast:
3	chr20:24988426..24991345-chr20:24993001..24995415,2	K562	blood:
4	chr20:24993871..24995608-chr20:24996954..24999019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1007881	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1056036	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11700073	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11905625	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1535042	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2008275	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2235847	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs227625	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs227633	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs227634	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs227650	1.00[JPT][hapmap]
rs227653	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs3746330	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41315094	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815351	1.00[JPT][hapmap]
rs4815357	1.00[JPT][hapmap]
rs6050201	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6050255	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6050259	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6050261	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6083699	1.00[JPT][hapmap]
rs6083709	1.00[JPT][hapmap]
rs60849220	0.90[EUR][1000 genomes]
rs6114980	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6114981	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6114984	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132775	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6132777	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6132778	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132783	0.83[ASN][1000 genomes]
rs6132784	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132785	0.93[ASN][1000 genomes]
rs6132788	0.96[EUR][1000 genomes]
rs6132789	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6132790	0.90[EUR][1000 genomes]
rs6138437	1.00[JPT][hapmap]
rs6138442	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138453	1.00[JPT][hapmap]
rs6138455	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138457	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138458	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6138460	0.83[ASN][1000 genomes]
rs6138463	0.88[ASN][1000 genomes]
rs6138464	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138465	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138466	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6138475	0.82[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs62217173	0.96[EUR][1000 genomes]
rs62217174	0.96[EUR][1000 genomes]
rs62217175	0.96[EUR][1000 genomes]
rs6707	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7268095	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs8125909	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs8183891	1.00[JPT][hapmap]

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	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
6	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr20:24981600-25003600	Weak transcription	Fetal Heart	heart
3	chr20:24981800-24997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:24983200-24996800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr20:24983200-25003800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr20:24983200-25005000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr20:24983200-25007800	Strong transcription	Primary T cells from cord blood	blood
8	chr20:24983200-25008200	Strong transcription	Primary B cells from cord blood	blood
9	chr20:24983400-24995400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:24983400-24996600	Strong transcription	Placenta	Placenta
11	chr20:24983800-24994800	Strong transcription	Primary hematopoietic stem cells	blood
12	chr20:24983800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr20:24984600-24997200	Strong transcription	Fetal Intestine Large	intestine
14	chr20:24985000-24997200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr20:24985000-24997600	Strong transcription	Fetal Intestine Small	intestine
16	chr20:24985000-25004400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr20:24985000-25005600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr20:24985200-24995800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr20:24985200-25002600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:24985200-25003200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr20:24985200-25007800	Strong transcription	Fetal Muscle Leg	muscle
22	chr20:24985600-24996600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr20:24985800-24995800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr20:24985800-24997200	Strong transcription	Lung	lung
25	chr20:24985800-24997600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr20:24985800-25002400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:24985800-25004200	Strong transcription	Thymus	Thymus
28	chr20:24985800-25004400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr20:24985800-25005000	Strong transcription	Adipose Nuclei	Adipose
30	chr20:24985800-25005800	Strong transcription	Spleen	Spleen
31	chr20:24985800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:24985800-25007600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr20:24985800-25007800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr20:24986000-24994800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr20:24986000-24996200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr20:24986000-25004800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr20:24986200-24994400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:24986200-25012400	Strong transcription	Dnd41	blood
39	chr20:24986400-24997000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr20:24986400-25003800	Strong transcription	Aorta	Aorta
41	chr20:24986400-25004400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr20:24986400-25012400	Weak transcription	Fetal Brain Male	brain
43	chr20:24986600-24995800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:24986600-24995800	Strong transcription	Fetal Thymus	thymus
45	chr20:24986600-24997400	Strong transcription	Ovary	ovary
46	chr20:24986800-24997200	Strong transcription	Brain Germinal Matrix	brain
47	chr20:24987000-24997400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr20:24987200-24996600	Strong transcription	Fetal Stomach	stomach
49	chr20:24987400-25005200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:24987600-25007800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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