Variant report

Variant	rs2783085
Chromosome Location	chr13:80321164-80321165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10507900	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11619959	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12019641	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12428029	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12867107	0.88[EUR][1000 genomes]
rs1335288	0.85[EUR][1000 genomes]
rs1414110	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2039554	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2039555	0.87[EUR][1000 genomes]
rs2039556	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2152226	0.86[EUR][1000 genomes]
rs2248409	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2248413	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248563	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2262460	0.89[EUR][1000 genomes]
rs2329137	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2329138	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2802634	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2802638	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2802640	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802641	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35661635	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4885658	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885660	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4885669	0.86[EUR][1000 genomes]
rs7322877	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7327527	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7984156	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs915260	0.87[EUR][1000 genomes]
rs9530958	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9530959	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9545191	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545203	0.87[EUR][1000 genomes]
rs9545205	0.87[EUR][1000 genomes]

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	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1039333	chr13:80289936-80333167	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2783085	HES2	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80309800-80324400	Weak transcription	Right Atrium	heart
2	chr13:80311400-80324000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:80311600-80323800	Weak transcription	HMEC	breast
4	chr13:80315400-80323000	Weak transcription	Fetal Muscle Leg	muscle
5	chr13:80315400-80324400	Weak transcription	Pancreas	Pancrea
6	chr13:80315400-80324400	Weak transcription	Small Intestine	intestine
7	chr13:80315800-80323000	Weak transcription	Fetal Heart	heart
8	chr13:80315800-80324600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:80317400-80322000	Weak transcription	Ovary	ovary
10	chr13:80317400-80323600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:80317400-80324000	Weak transcription	NHEK	skin
12	chr13:80319200-80324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:80319400-80322800	Weak transcription	Fetal Kidney	kidney
14	chr13:80319600-80324000	Weak transcription	Fetal Stomach	stomach
15	chr13:80319600-80330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:80319800-80322800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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