Variant report

Variant	rs17705904
Chromosome Location	chr20:15770794-15770795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11697766	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11700387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16996498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16996594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16996600	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs16996618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16996626	0.91[CEU][hapmap]
rs17626441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17632947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17704936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1990396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41439350	0.91[CEU][hapmap]
rs4813193	0.83[CEU][hapmap]
rs55755745	0.87[EUR][1000 genomes]
rs6043534	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131725	0.91[CEU][hapmap]
rs6135515	0.83[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6135552	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs6135553	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs62194689	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62194715	0.89[EUR][1000 genomes]
rs62194718	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7266511	0.83[CEU][hapmap]
rs7270597	0.83[CEU][hapmap]
rs73097220	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73097238	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763659	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs763661	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv833928	chr20:15619962-15780758	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv458934	chr20:15738086-15772582	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv585641	chr20:15738086-15772582	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv585642	chr20:15738086-15772876	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv519883	chr20:15738086-15817106	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv585643	chr20:15759361-15796051	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv912793	chr20:15760969-15807441	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv833929	chr20:15765372-15977337	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1847965	chr20:15766727-15807441	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv585644	chr20:15766727-15807441	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17705904	TASP1	cis	cerebellum	SCAN
rs17705904	DSTN	cis	parietal	SCAN
rs17705904	C20orf72	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15767200-15770800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr20:15770000-15770800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr20:15770000-15775000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:15770000-15775200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:15770200-15773400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr20:15770200-15773600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr20:15770200-15773800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr20:15770200-15775000	Weak transcription	Brain Germinal Matrix	brain
9	chr20:15770200-15775200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr20:15770200-15775800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:15770200-15776400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr20:15770400-15771200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr20:15770400-15773600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr20:15770600-15775000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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