Variant report

Variant	rs4815364
Chromosome Location	chr20:25035711-25035712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25034947..25037572-chr20:25052854..25054680,2	MCF-7	breast:
2	chr20:25033407..25037735-chr20:25037828..25040328,4	MCF-7	breast:
3	chr20:25027984..25032783-chr20:25034265..25037344,6	MCF-7	breast:
4	chr20:25024429..25027041-chr20:25035643..25038257,2	K562	blood:
5	chr20:25026036..25030944-chr20:25033529..25038477,7	MCF-7	breast:
6	chr20:24973677..24976371-chr20:25035249..25037062,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2387577	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs4815365	1.00[ASN][1000 genomes]
rs4815366	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs6083730	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6106989	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6115015	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6115024	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs6132792	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs910527	0.91[CHD][hapmap];0.87[JPT][hapmap]

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	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4815364	VSX1	cis	cerebellum	SCAN
rs4815364	ACSS1	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25020600-25037400	Enhancers	Psoas Muscle	Psoas
2	chr20:25027800-25037000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:25028600-25037200	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr20:25028800-25036600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:25028800-25037200	Enhancers	Aorta	Aorta
6	chr20:25029000-25036800	Enhancers	Right Ventricle	heart
7	chr20:25029200-25037200	Enhancers	Fetal Muscle Trunk	muscle
8	chr20:25031800-25035800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:25031800-25037000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr20:25032000-25037600	Enhancers	Spleen	Spleen
11	chr20:25032200-25036000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr20:25032200-25036000	Genic enhancers	Fetal Intestine Large	intestine
13	chr20:25032200-25036600	Enhancers	Ovary	ovary
14	chr20:25032200-25037400	Enhancers	Stomach Mucosa	stomach
15	chr20:25032400-25035800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:25032400-25036400	Genic enhancers	Fetal Intestine Small	intestine
17	chr20:25032400-25037000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr20:25032400-25037000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr20:25032400-25037000	Genic enhancers	Fetal Stomach	stomach
20	chr20:25032400-25037200	Enhancers	Small Intestine	intestine
21	chr20:25032400-25037400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:25032600-25037200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr20:25032600-25037200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr20:25032800-25036000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr20:25033000-25036800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr20:25033000-25037200	Enhancers	Fetal Thymus	thymus
27	chr20:25033000-25037400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:25033200-25035800	Enhancers	HSMMtube	muscle
29	chr20:25033200-25036800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr20:25033200-25036800	Enhancers	Pancreas	Pancrea
31	chr20:25033400-25037200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr20:25033600-25037400	Enhancers	NHDF-Ad	bronchial
33	chr20:25033800-25037200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr20:25034000-25036200	Enhancers	HepG2	liver
35	chr20:25034000-25037200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr20:25034200-25035800	Enhancers	Fetal Kidney	kidney
37	chr20:25034200-25036800	Enhancers	Colonic Mucosa	Colon
38	chr20:25034200-25037800	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr20:25034400-25035800	Weak transcription	Osteobl	bone
40	chr20:25034400-25036000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr20:25034400-25036800	Enhancers	Liver	Liver
42	chr20:25034600-25036400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr20:25034600-25036400	Genic enhancers	Dnd41	blood
44	chr20:25034600-25036800	Enhancers	Right Atrium	heart
45	chr20:25034600-25037200	Enhancers	Lung	lung
46	chr20:25034600-25037200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr20:25034600-25037200	Enhancers	Thymus	Thymus
48	chr20:25034800-25036200	Genic enhancers	Left Ventricle	heart
49	chr20:25034800-25036400	Genic enhancers	Placenta	Placenta
50	chr20:25034800-25036600	Enhancers	Rectal Mucosa Donor 29	rectum

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