Variant report

Variant	rs1568209
Chromosome Location	chr15:92581290-92581291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10520702	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11074035	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11074036	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11074039	0.88[CEU][hapmap]
rs11632297	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55986834	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59528323	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs908652	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs992836	0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][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	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv570451	chr15:92575841-92581290	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv570456	chr15:92577382-92581290	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1568209	C15orf58	cis	parietal	SCAN
rs1568209	SLCO3A1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92574200-92585800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:92574800-92585800	Weak transcription	Pancreas	Pancrea
3	chr15:92575600-92584000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:92575800-92584400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:92576000-92583800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:92577000-92586600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:92577400-92584400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:92578000-92583800	Weak transcription	Esophagus	oesophagus
9	chr15:92578000-92583800	Weak transcription	Right Atrium	heart
10	chr15:92578000-92584800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:92578000-92585600	Weak transcription	Spleen	Spleen
12	chr15:92578200-92583800	Weak transcription	Fetal Heart	heart
13	chr15:92578800-92581400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:92579000-92587000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:92579200-92583800	Weak transcription	Brain Substantia Nigra	brain
16	chr15:92579200-92583800	Weak transcription	Right Ventricle	heart
17	chr15:92579200-92585200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:92579400-92584400	Weak transcription	Brain Angular Gyrus	brain
19	chr15:92579400-92585200	Weak transcription	Left Ventricle	heart
20	chr15:92579400-92585200	Weak transcription	Lung	lung
21	chr15:92579400-92591200	Weak transcription	Ovary	ovary
22	chr15:92580200-92581400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:92580400-92581400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr15:92580400-92581400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr15:92580400-92581400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:92580600-92581400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr15:92580600-92581400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr15:92580600-92581400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr15:92580800-92581400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr15:92581000-92581400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr15:92581000-92581400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr15:92581000-92581400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:92581000-92593400	Weak transcription	Aorta	Aorta
34	chr15:92581200-92581400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:92581200-92586600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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