Variant report

Variant	rs4755306
Chromosome Location	chr11:45310410-45310411
allele	G/T
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	REST	chr11:45309455-45310855	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr11:45309621-45310440	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr11:45309720-45310457	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45305084..45308064-chr11:45308692..45311186,2	K562	blood:

Variant related genes	Relation type
SYT13	TF binding region
ENSG00000019505	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1075778	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769133	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769134	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769135	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769136	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1077490	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077491	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838437	0.83[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10838438	0.87[ASN][1000 genomes]
rs11038354	0.80[JPT][hapmap]
rs11038358	0.80[JPT][hapmap]
rs11038360	0.87[JPT][hapmap]
rs11038372	0.88[ASN][1000 genomes]
rs11038382	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11038384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604409	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12363398	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363412	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289448	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2863176	0.87[JPT][hapmap]
rs2863178	0.83[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2863181	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2863182	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902429	0.82[ASN][1000 genomes]
rs2902433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34191816	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758726	0.80[JPT][hapmap]
rs4556529	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4556531	0.87[JPT][hapmap]
rs4755943	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4992029	0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs6485603	0.87[JPT][hapmap]
rs6485605	0.84[ASN][1000 genomes]
rs6485607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485609	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110580	0.87[JPT][hapmap]
rs7114339	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117240	0.81[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7118844	0.81[EUR][1000 genomes]
rs7123438	0.81[EUR][1000 genomes]
rs7123698	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7123765	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7127746	0.87[JPT][hapmap]
rs7130748	0.81[EUR][1000 genomes]
rs7131174	0.81[EUR][1000 genomes]
rs731102	0.85[JPT][hapmap]
rs7395289	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7395357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7395419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7395421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480175	0.81[EUR][1000 genomes]
rs751196	0.89[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7943596	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8929	0.87[JPT][hapmap]
rs9300051	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[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	nsv530619	chr11:45294176-45553928	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4755306	LRP4	cis	cerebellum	SCAN
rs4755306	F2	cis	cerebellum	SCAN
rs4755306	SYT13	cis	Skin Sun Exposed Lower leg	GTEx
rs4755306	SYT13	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45308400-45311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:45308800-45312400	Weak transcription	Fetal Intestine Large	intestine
3	chr11:45309600-45310600	Enhancers	Fetal Brain Male	brain
4	chr11:45309600-45310800	Enhancers	Brain Germinal Matrix	brain
5	chr11:45310200-45310600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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