Variant report

Variant	rs13251735
Chromosome Location	chr8:102830075-102830076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10091905	0.83[CEU][hapmap]
rs10094868	0.83[CEU][hapmap]
rs10216921	0.83[CEU][hapmap]
rs10505012	0.83[CEU][hapmap]
rs1073373	0.88[CEU][hapmap]
rs1074703	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1077500	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1077998	0.82[CEU][hapmap]
rs10808377	0.83[CEU][hapmap]
rs10808378	0.82[CEU][hapmap]
rs10808379	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10955274	0.87[CEU][hapmap]
rs1111884	0.83[CEU][hapmap]
rs1111886	0.88[CEU][hapmap]
rs11782123	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs12334693	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12545537	0.83[CEU][hapmap]
rs12550570	0.83[CEU][hapmap]
rs1264930	0.88[CEU][hapmap]
rs1264933	1.00[CEU][hapmap]
rs12677525	0.88[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs13255004	0.96[EUR][1000 genomes]
rs13268186	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13281055	0.83[CEU][hapmap]
rs1465167	0.83[CEU][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1557336	0.88[CEU][hapmap]
rs17406994	0.87[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1893366	1.00[CEU][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs2032121	0.83[CEU][hapmap]
rs2154652	0.83[CEU][hapmap]
rs2155938	0.88[CEU][hapmap]
rs2155942	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2155943	0.92[EUR][1000 genomes]
rs2186392	0.83[CEU][hapmap]
rs2186393	0.83[CEU][hapmap]
rs2212701	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2226724	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs2226725	0.95[EUR][1000 genomes]
rs2387616	0.83[CEU][hapmap]
rs2387618	0.83[CEU][hapmap]
rs2387619	0.83[CEU][hapmap]
rs28837777	0.85[EUR][1000 genomes]
rs2892324	0.85[CEU][hapmap]
rs4576401	0.85[EUR][1000 genomes]
rs4734040	0.83[CEU][hapmap]
rs4734593	0.83[CEU][hapmap]
rs4734594	0.83[CEU][hapmap]
rs4734595	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs4734596	0.86[EUR][1000 genomes]
rs4734597	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6468793	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6468794	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6468795	0.88[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6468796	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6468798	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6468799	0.88[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs6468801	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6984260	0.88[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6988793	0.83[CEU][hapmap];0.87[CHD][hapmap];0.82[TSI][hapmap]
rs6993577	0.96[EUR][1000 genomes]
rs6997574	0.83[CEU][hapmap]
rs7000357	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7001437	0.83[CEU][hapmap]
rs7002547	0.83[CEU][hapmap]
rs7003041	0.87[MEX][hapmap]
rs7008826	0.83[CEU][hapmap]
rs7009385	0.83[CEU][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7011941	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7012512	0.87[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7015311	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7017754	0.88[CEU][hapmap];0.82[CHD][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs7813132	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7827304	0.80[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7827691	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7827941	0.88[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7829693	0.83[MEX][hapmap]
rs7830291	0.83[CEU][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7835223	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7835485	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7838696	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7844292	0.87[MEX][hapmap]
rs8181022	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs8181025	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9297313	1.00[CEU][hapmap]
rs9693504	0.82[CEU][hapmap]
rs9693531	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13251735	NCALD	cis	parietal	SCAN
rs13251735	C8orf56	cis	parietal	SCAN
rs13251735	FOXL1	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102803600-102870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:102828400-102832600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:102829000-102830800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:102829400-102830200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr8:102829400-102830200	Enhancers	Brain Germinal Matrix	brain
6	chr8:102829400-102830200	Active TSS	Brain Hippocampus Middle	brain
7	chr8:102829400-102830800	Enhancers	Aorta	Aorta
8	chr8:102829400-102830800	Enhancers	Fetal Muscle Leg	muscle
9	chr8:102829400-102830800	Enhancers	Ovary	ovary
10	chr8:102829600-102830200	Active TSS	Brain Anterior Caudate	brain
11	chr8:102829600-102830200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr8:102829600-102830200	Enhancers	Fetal Brain Female	brain
13	chr8:102829600-102830400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr8:102829600-102830800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:102829600-102830800	Enhancers	Brain Substantia Nigra	brain
16	chr8:102829600-102834600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:102829800-102830200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr8:102829800-102830200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:102829800-102830200	Active TSS	Brain Cingulate Gyrus	brain
20	chr8:102829800-102830400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:102829800-102830400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:102829800-102830400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr8:102829800-102830800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:102830000-102830200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr8:102830000-102830200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr8:102830000-102830200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:102830000-102830200	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr8:102830000-102830200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr8:102830000-102830400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr8:102830000-102830800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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