Variant report

Variant	rs6013845
Chromosome Location	chr20:52566271-52566272
allele	G/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
2	chr17:56707619..56710170-chr20:52565363..52567557,2	MCF-7	breast:
3	chr20:52565008..52572229-chr20:55837900..55845361,9	MCF-7	breast:
4	chr17:59804481..59806833-chr20:52566081..52568300,2	MCF-7	breast:
5	chr17:57919574..57922169-chr20:52565236..52567154,2	MCF-7	breast:
6	chr20:52565783..52568292-chr3:178833471..178835400,2	MCF-7	breast:
7	chr20:52565056..52568176-chr20:55835450..55837434,3	MCF-7	breast:
8	chr17:59955749..59958529-chr20:52564556..52567164,2	MCF-7	breast:
9	chr20:52565107..52568649-chr20:52823684..52826196,6	MCF-7	breast:
10	chr17:59938630..59941732-chr20:52564272..52566686,3	MCF-7	breast:
11	chr20:52564545..52567284-chr20:52704374..52707126,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000136492	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1055251	0.82[TSI][hapmap]
rs6013844	0.88[ASW][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs719204	0.82[CEU][hapmap]
rs732377	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6013845	ATP9A	cis	cerebellum	SCAN
rs6013845	CSTF1	cis	cerebellum	SCAN
rs6013845	BMP7	cis	parietal	SCAN
rs6013845	FAM65C	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52557400-52569200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr20:52558400-52569000	Weak transcription	Fetal Intestine Small	intestine
3	chr20:52564000-52567200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr20:52564200-52567400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr20:52564200-52576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:52564600-52567000	Enhancers	Primary hematopoietic stem cells	blood
7	chr20:52564600-52567400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr20:52564800-52567000	Enhancers	Fetal Thymus	thymus
9	chr20:52565000-52567000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:52565000-52567000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:52565000-52567000	Enhancers	Primary B cells from peripheral blood	blood
12	chr20:52565000-52567000	Enhancers	Left Ventricle	heart
13	chr20:52565000-52567000	Enhancers	Lung	lung
14	chr20:52565000-52567000	Enhancers	Thymus	Thymus
15	chr20:52565000-52567000	Enhancers	Spleen	Spleen
16	chr20:52565000-52567000	Enhancers	HMEC	breast
17	chr20:52565200-52566400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr20:52565200-52566400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr20:52565200-52566400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr20:52565200-52566400	Genic enhancers	Rectal Mucosa Donor 29	rectum
21	chr20:52565200-52566400	Enhancers	Small Intestine	intestine
22	chr20:52565200-52566400	Enhancers	Hela-S3	cervix
23	chr20:52565200-52566600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr20:52565200-52566600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:52565200-52566800	Enhancers	HUVEC	blood vessel
26	chr20:52565200-52566800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr20:52565200-52567000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr20:52565200-52567000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr20:52565200-52567000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:52565200-52567000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:52565200-52567000	Enhancers	Duodenum Mucosa	Duodenum
32	chr20:52565200-52567000	Enhancers	Fetal Muscle Trunk	muscle
33	chr20:52565200-52567000	Enhancers	NHEK	skin
34	chr20:52565200-52567400	Enhancers	NHDF-Ad	bronchial
35	chr20:52565400-52566400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:52565400-52566400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr20:52565400-52566400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr20:52565400-52566400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr20:52565400-52566400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr20:52565400-52566400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:52565400-52566400	Enhancers	Adipose Nuclei	Adipose
42	chr20:52565400-52566400	Genic enhancers	Gastric	stomach
43	chr20:52565400-52566400	Genic enhancers	Rectal Mucosa Donor 31	rectum
44	chr20:52565400-52566400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr20:52565400-52566400	Flanking Active TSS	Dnd41	blood
46	chr20:52565400-52566400	Flanking Active TSS	Osteobl	bone
47	chr20:52565400-52566600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:52565400-52566600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:52565400-52566800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr20:52565400-52566800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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