Variant report

Variant	rs6115013
Chromosome Location	chr20:25024879-25024880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25024429..25027041-chr20:25035643..25038257,2	K562	blood:
2	chr20:25022614..25025327-chr20:25028235..25031123,4	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs6050267	1.00[ASN][1000 genomes]
rs6076312	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083725	0.94[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083726	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083728	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083729	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115009	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115010	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115011	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217192	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273310	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6115013	SSTR4	cis	parietal	SCAN
rs6115013	ADAM23	trans	lymphoblastoid	seeQTL
rs6115013	CST5	cis	cerebellum	SCAN
rs6115013	ACSS1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
2	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
3	chr20:25014000-25026400	Enhancers	Brain Cingulate Gyrus	brain
4	chr20:25014200-25026400	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr20:25014400-25025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:25016400-25025800	Enhancers	Fetal Heart	heart
7	chr20:25016600-25025400	Enhancers	Fetal Muscle Leg	muscle
8	chr20:25016600-25027600	Enhancers	Right Atrium	heart
9	chr20:25016600-25034800	Weak transcription	A549	lung
10	chr20:25017000-25026600	Enhancers	Brain Anterior Caudate	brain
11	chr20:25017400-25026400	Enhancers	Brain Substantia Nigra	brain
12	chr20:25017600-25026400	Enhancers	Left Ventricle	heart
13	chr20:25017800-25029000	Genic enhancers	Placenta	Placenta
14	chr20:25017800-25034200	Weak transcription	Fetal Kidney	kidney
15	chr20:25018600-25025600	Enhancers	Liver	Liver
16	chr20:25020200-25026400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr20:25020600-25025000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr20:25020600-25027000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:25020600-25037400	Enhancers	Psoas Muscle	Psoas
20	chr20:25021200-25025000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:25021200-25025400	Weak transcription	Fetal Brain Female	brain
22	chr20:25021200-25027200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr20:25021200-25032600	Weak transcription	NHDF-Ad	bronchial
24	chr20:25021400-25026400	Enhancers	Adipose Nuclei	Adipose
25	chr20:25022200-25027000	Weak transcription	Ovary	ovary
26	chr20:25022200-25033000	Weak transcription	Brain Germinal Matrix	brain
27	chr20:25022400-25026000	Enhancers	Brain Hippocampus Middle	brain
28	chr20:25022600-25025600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr20:25022600-25026000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr20:25022600-25026400	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr20:25023000-25025800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr20:25023000-25026200	Enhancers	Esophagus	oesophagus
33	chr20:25023000-25026400	Enhancers	Aorta	Aorta
34	chr20:25023600-25026400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr20:25023600-25026600	Enhancers	Primary B cells from cord blood	blood
36	chr20:25023800-25025200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25023800-25025400	Enhancers	Stomach Smooth Muscle	stomach
38	chr20:25023800-25026800	Enhancers	Primary B cells from peripheral blood	blood
39	chr20:25023800-25027000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr20:25023800-25027200	Weak transcription	Stomach Mucosa	stomach
41	chr20:25024000-25025000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr20:25024000-25025800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr20:25024000-25026200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:25024000-25032400	Weak transcription	Small Intestine	intestine
45	chr20:25024200-25025400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr20:25024200-25025400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr20:25024200-25025400	Weak transcription	Gastric	stomach
48	chr20:25024200-25025600	Weak transcription	Primary T cells from cord blood	blood
49	chr20:25024200-25025600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr20:25024200-25026000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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