Variant report

Variant	rs17466480
Chromosome Location	chr15:77390870-77390871
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	chr15:77390348..77392249-chr15:77393054..77395788,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1015813	0.80[ASN][1000 genomes]
rs10519158	0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11853625	0.84[ASN][1000 genomes]
rs11853633	0.91[ASN][1000 genomes]
rs11854182	0.91[ASN][1000 genomes]
rs11856513	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11856538	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857330	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs12148274	0.83[EUR][1000 genomes]
rs12324366	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12900110	0.85[EUR][1000 genomes]
rs12902106	0.86[EUR][1000 genomes]
rs12902434	0.85[EUR][1000 genomes]
rs12902446	0.92[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912963	0.84[EUR][1000 genomes]
rs13379686	0.93[ASN][1000 genomes]
rs13380152	0.86[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs1374201	0.86[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs1446313	0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs16968730	0.96[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs17381652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17381821	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs17383078	0.89[ASN][1000 genomes]
rs1867780	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2044453	0.96[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2292594	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.84[ASN][1000 genomes]
rs2864079	0.80[ASN][1000 genomes]
rs34572155	0.96[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs35093280	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4592615	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs4638539	0.89[ASN][1000 genomes]
rs4886514	0.85[EUR][1000 genomes]
rs4886852	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs55881066	0.84[ASN][1000 genomes]
rs59831220	0.91[ASN][1000 genomes]
rs60761381	0.80[ASN][1000 genomes]
rs60863150	0.84[ASN][1000 genomes]
rs7163620	0.83[EUR][1000 genomes]
rs7173670	0.91[ASN][1000 genomes]
rs7182221	0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap]
rs74025074	0.93[ASN][1000 genomes]
rs74027548	0.84[ASN][1000 genomes]
rs74027549	0.82[ASN][1000 genomes]
rs7496431	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17466480	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs17466480	PSTPIP1	cis	multi-tissue	Pritchard
rs17466480	CYP1A2	cis	cerebellum	SCAN
rs17466480	HMG20A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77376800-77395600	Weak transcription	Fetal Intestine Small	intestine
2	chr15:77378600-77392000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:77387000-77404200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:77389200-77393400	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:77389200-77396200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:77389400-77393200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:77390200-77393400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:77390200-77395800	Weak transcription	Spleen	Spleen
9	chr15:77390200-77404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:77390400-77393200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:77390400-77396200	Weak transcription	Fetal Stomach	stomach
12	chr15:77390400-77396400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:77390400-77406400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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