Variant report

Variant	rs8075585
Chromosome Location	chr17:59949487-59949488
allele	A/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59938592..59943097-chr17:59943271..59951102,13	K562	blood:
2	chr17:59487241..59490325-chr17:59947860..59950817,3	MCF-7	breast:
3	chr17:59948535..59950391-chr3:64389921..64392537,2	MCF-7	breast:
4	chr1:210545342..210547674-chr17:59947444..59950417,2	MCF-7	breast:
5	chr17:59947167..59950048-chr20:55745126..55747472,2	MCF-7	breast:
6	chr17:59945351..59947710-chr17:59948808..59951151,2	K562	blood:
7	chr17:59949335..59951629-chr17:60003040..60005036,2	MCF-7	breast:
8	chr17:59947273..59949917-chr20:55800164..55802444,2	MCF-7	breast:
9	chr17:59947480..59950450-chr20:52574915..52576530,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000136492	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10515212	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11654581	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11656805	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452044	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12452396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453935	0.87[CEU][hapmap]
rs12602103	0.88[CEU][hapmap]
rs17542001	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17614124	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014444	1.00[YRI][hapmap]
rs2066962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278813	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4968453	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4988340	0.82[ASW][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs56267713	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294609	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56391142	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58426748	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504074	0.88[CEU][hapmap]
rs7223607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843728	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843731	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843735	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843752	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843757	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8076727	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8076746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8075585	MRPS23	cis	parietal	SCAN
rs8075585	LPO	cis	cerebellum	SCAN
rs8075585	PTRH2	cis	cerebellum	SCAN
rs8075585	BRIP1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941200-59957000	Weak transcription	Spleen	Spleen
2	chr17:59941200-59964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:59941400-59953200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:59941400-59953200	Weak transcription	Small Intestine	intestine
5	chr17:59941400-59957000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:59941400-59957600	Weak transcription	Gastric	stomach
7	chr17:59941400-59965400	Weak transcription	Lung	lung
8	chr17:59941400-59975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
11	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
12	chr17:59941600-59953200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:59941600-59957000	Weak transcription	Esophagus	oesophagus
14	chr17:59941600-59957000	Weak transcription	Thymus	Thymus
15	chr17:59941600-59965200	Weak transcription	Psoas Muscle	Psoas
16	chr17:59941600-59965400	Weak transcription	Brain Substantia Nigra	brain
17	chr17:59941600-59965600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:59941600-59966800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
21	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
22	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
23	chr17:59941800-59952200	Weak transcription	Osteobl	bone
24	chr17:59941800-59953200	Weak transcription	HSMMtube	muscle
25	chr17:59941800-59954200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr17:59941800-59957000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:59941800-59960000	Weak transcription	NHEK	skin
28	chr17:59941800-59961000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:59941800-59967000	Weak transcription	Fetal Brain Male	brain
30	chr17:59941800-59968800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:59941800-59969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr17:59941800-59971800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
35	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:59943600-59962200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:59943800-59949800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:59943800-59950000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:59943800-59950200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:59943800-59956800	Strong transcription	HSMM	muscle
42	chr17:59944200-59949800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:59944200-59949800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:59944200-59950000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr17:59944200-59950000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:59944400-59949800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr17:59944400-59949800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:59944400-59949800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:59944400-59949800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:59944400-59949800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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