Variant report

Variant	rs733299
Chromosome Location	chr15:40767739-40767740
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40764613..40768482-chr15:40771207..40776375,6	K562	blood:
2	chr15:40743208..40745711-chr15:40766264..40768804,2	MCF-7	breast:
3	chr15:40765795..40768318-chr15:40771145..40773484,3	MCF-7	breast:
4	chr15:40761851..40766417-chr15:40767472..40770724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169105	Chromatin interaction
ENSG00000244251	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1051482	0.83[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs10851396	0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs11070279	0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs11852527	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11853333	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs11857247	0.88[CEU][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12148185	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12898690	0.83[AMR][1000 genomes]
rs12907448	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs12908114	0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs12915563	1.00[YRI][hapmap]
rs12916323	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1453183	0.83[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1901774	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2123534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412524	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3213999	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35030447	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36122190	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457966	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs61048252	0.86[EUR][1000 genomes]
rs62018030	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62018046	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62018048	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62018051	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7164385	0.87[EUR][1000 genomes]
rs7181909	0.87[EUR][1000 genomes]
rs72733469	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs731640	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025458	0.83[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs8028910	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9672313	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9806410	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs9972363	0.81[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs999197	0.88[CEU][hapmap];0.85[EUR][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs733299	IVD	cis	cerebellum	SCAN
rs733299	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs733299	C15orf57	cis	Artery Tibial	GTEx
rs733299	C15orf57	cis	cerebellum	SCAN
rs733299	C15orf23	cis	cerebellum	SCAN
rs733299	CCDC32	cis	lesional skin	skin_eQTL
rs733299	C15orf57	cis	Nerve Tibial	GTEx
rs733299	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs733299	LPCAT4	cis	parietal	SCAN
rs733299	RP11-111A22.1	cis	lung	GTEx
rs733299	ZFYVE19	cis	parietal	SCAN
rs733299	C15orf57	cis	Esophagus Muscularis	GTEx
rs733299	C15orf57	cis	Adipose Subcutaneous	GTEx
rs733299	ZFYVE19	cis	cerebellum	SCAN
rs733299	C15orf57	cis	Cerebellum	GTEx
rs733299	KNSTRN	cis	Heart Left Ventricle	GTEx
rs733299	C15orf57	cis	parietal	SCAN
rs733299	RP11-111A22.1	cis	Artery Tibial	GTEx
rs733299	PLA2G4E	cis	parietal	SCAN
rs733299	CCDC32	cis	normal skin	skin_eQTL
rs733299	C15orf57	cis	lymphoblastoid	seeQTL
rs733299	C15orf23	cis	parietal	SCAN
rs733299	MRPL42P5	cis	multi-tissue	Pritchard
rs733299	C15orf57	cis	lung	GTEx
rs733299	CCDC32	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40763000-40770200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40764600-40768200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:40764600-40769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:40764600-40770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:40764600-40770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:40764600-40771400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:40764800-40770000	Weak transcription	NHEK	skin
8	chr15:40765000-40769800	Weak transcription	Hela-S3	cervix
9	chr15:40765000-40772400	Weak transcription	Esophagus	oesophagus
10	chr15:40765000-40773400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:40765200-40768400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:40765200-40770200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:40765200-40770800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40765600-40768400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:40766600-40770000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:40766800-40769800	Weak transcription	K562	blood
17	chr15:40767200-40769000	Weak transcription	Fetal Stomach	stomach
18	chr15:40767400-40769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:40767600-40771400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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