Variant report

Variant	rs17360083
Chromosome Location	chr15:83570081-83570082
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr15:83569905-83570229	HepG2	liver:	n/a	n/a
2	FOXA1	chr15:83569908-83570305	HepG2	liver:	n/a	n/a
3	FOXA1	chr15:83569923-83570333	HepG2	liver:	n/a	n/a
4	FOXA1	chr15:83569841-83570221	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HOMER2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10906985	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11259959	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12385964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1256429	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1256434	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256451	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256452	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1256453	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256455	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12905235	0.86[JPT][hapmap]
rs13380133	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1553883	0.86[JPT][hapmap]
rs2379992	0.86[JPT][hapmap]
rs2621227	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621228	0.92[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667382	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2667383	0.94[ASN][1000 genomes]
rs2667385	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41310978	0.99[ASN][1000 genomes]
rs4238539	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs62011731	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62011732	0.94[ASN][1000 genomes]
rs62011734	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168760	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169401	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038679	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9806543	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522673	chr15:83565711-83570114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17360083	BTBD1	cis	cerebellum	SCAN
rs17360083	RASGRF1	cis	parietal	SCAN
rs17360083	RASGRF1	cis	cerebellum	SCAN
rs17360083	WHAMM	cis	Adipose Subcutaneous	GTEx
rs17360083	HOMER2	cis	Skin Sun Exposed Lower leg	GTEx
rs17360083	EFTUD1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
2	chr15:83559600-83570200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:83560400-83570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:83567800-83570400	Enhancers	Psoas Muscle	Psoas
5	chr15:83568200-83570800	Enhancers	Pancreas	Pancrea
6	chr15:83568200-83585400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:83569200-83570200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:83569200-83570400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr15:83569200-83571600	Enhancers	Liver	Liver
10	chr15:83569400-83570400	Enhancers	HSMMtube	muscle
11	chr15:83569400-83570600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:83569400-83571000	Enhancers	HepG2	liver
13	chr15:83569600-83570800	Enhancers	Gastric	stomach
14	chr15:83569800-83570200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:83569800-83570200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:83569800-83570400	Enhancers	Left Ventricle	heart
17	chr15:83569800-83570400	Enhancers	Right Ventricle	heart
18	chr15:83570000-83570400	Enhancers	Brain Hippocampus Middle	brain
19	chr15:83570000-83570600	Active TSS	Pancreatic Islets	Pancreatic Islet

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