Variant report

Variant	rs6485607
Chromosome Location	chr11:45306531-45306532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1075778	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769133	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769134	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769135	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1077490	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077491	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838437	0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10838438	0.87[ASN][1000 genomes]
rs11038360	0.87[JPT][hapmap]
rs11038372	0.88[ASN][1000 genomes]
rs11038382	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11038384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11604409	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12363398	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363412	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2863176	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2863178	0.88[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2863181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2863182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902429	0.82[ASN][1000 genomes]
rs2902433	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34191816	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4556529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4556531	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs4755306	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]
rs4755943	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs4992029	0.87[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs6485603	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs6485605	0.84[ASN][1000 genomes]
rs6485608	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485609	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7110580	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs7114339	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117240	0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7118844	0.81[EUR][1000 genomes]
rs7119605	0.80[JPT][hapmap]
rs7123438	0.81[EUR][1000 genomes]
rs7123698	0.86[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	0.82[CHB][hapmap];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];0.95[ASN][1000 genomes]
rs7395357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395421	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];1.00[EUR][1000 genomes];0.98[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];0.98[ASN][1000 genomes]
rs7480175	0.81[EUR][1000 genomes]
rs751196	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7943596	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8929	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9300051	0.88[CHB][hapmap];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6485607	SYT13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45304000-45306800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45305000-45308200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr11:45305800-45306600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr11:45306000-45306600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:45306000-45306600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr11:45306000-45307600	Enhancers	Spleen	Spleen
7	chr11:45306000-45308000	Bivalent/Poised TSS	Fetal Brain Female	brain
8	chr11:45306000-45308400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
9	chr11:45306000-45308600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:45306200-45306600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:45306200-45306600	Active TSS	Fetal Intestine Large	intestine
12	chr11:45306200-45306800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:45306400-45306600	Enhancers	Fetal Intestine Small	intestine
14	chr11:45306400-45306800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:45306400-45307600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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