Variant report

Variant	rs9571716
Chromosome Location	chr13:67711345-67711346
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:67710572..67712224-chr13:67713182..67714868,2	K562	blood:
2	chr13:67685964..67690654-chr13:67706296..67711657,6	K562	blood:
3	chr13:67686001..67691093-chr13:67707345..67712221,5	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1927826	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs260152	0.87[JPT][hapmap];0.86[MEX][hapmap]
rs260153	0.87[JPT][hapmap]
rs4142274	0.93[MEX][hapmap]
rs7327414	0.82[CEU][hapmap]
rs7336017	0.81[CHD][hapmap]
rs9317640	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9317641	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9540981	0.93[MEX][hapmap]
rs9571713	0.87[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv430581	chr13:67572850-67762288	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv430582	chr13:67589898-67762299	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1037217	chr13:67589937-67728156	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1039600	chr13:67593961-67726047	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv541823	chr13:67593961-67726047	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1053514	chr13:67687520-67775011	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs9571716	IMP5	trans	brain	seeQTL
rs9571716	BEX5	trans	brain	seeQTL
rs9571716	GABBR2	trans	brain	seeQTL
rs9571716	IDH3B	trans	brain	seeQTL
rs9571716	HPS5	trans	brain	seeQTL
rs9571716	MN1	trans	brain	seeQTL
rs9571716	TRIM6	trans	brain	seeQTL
rs9571716	SUOX	trans	brain	seeQTL
rs9571716	GTF3C4	trans	brain	seeQTL
rs9571716	KIR2DL1	trans	brain	seeQTL
rs9571716	CAMK2G	trans	brain	seeQTL
rs9571716	ACOT7	trans	brain	seeQTL
rs9571716	TMEM155	trans	brain	seeQTL
rs9571716	TMEM55B	trans	brain	seeQTL
rs9571716	TMEM38B	trans	brain	seeQTL
rs9571716	EGFL6	trans	brain	seeQTL
rs9571716	CLTA	trans	brain	seeQTL
rs9571716	CPNE9	trans	brain	seeQTL
rs9571716	DNAJA3	trans	brain	seeQTL
rs9571716	SCYL1	trans	brain	seeQTL
rs9571716	INGX	trans	brain	seeQTL
rs9571716	HACL1	trans	brain	seeQTL
rs9571716	CCK	trans	brain	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67709000-67711400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:67709000-67711400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:67709000-67711400	Weak transcription	HSMM	muscle
4	chr13:67709000-67711400	Weak transcription	HSMMtube	muscle
5	chr13:67709200-67711400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:67709200-67711400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:67709200-67711600	Weak transcription	HUVEC	blood vessel
8	chr13:67709400-67717800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:67709800-67711400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr13:67710000-67712000	Enhancers	Liver	Liver
11	chr13:67710200-67712600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:67710200-67721000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr13:67710400-67712600	Enhancers	K562	blood
14	chr13:67710400-67715000	Enhancers	A549	lung
15	chr13:67710600-67711400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:67710600-67711600	Weak transcription	Brain Angular Gyrus	brain
17	chr13:67710600-67711600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr13:67710600-67711800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:67710600-67712200	Enhancers	Fetal Heart	heart
20	chr13:67710600-67712400	Enhancers	Brain Hippocampus Middle	brain
21	chr13:67710600-67712400	Weak transcription	Gastric	stomach
22	chr13:67710600-67713600	Weak transcription	Right Atrium	heart
23	chr13:67710800-67711400	Weak transcription	Fetal Lung	lung
24	chr13:67711000-67711400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:67711000-67711400	Weak transcription	Brain Substantia Nigra	brain
26	chr13:67711000-67712800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:67711200-67712600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr13:67711200-67714200	Enhancers	Brain Anterior Caudate	brain

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