Variant report

Variant	rs2802641
Chromosome Location	chr13:80323955-80323956
allele	A/G
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	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11619959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12019641	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12428029	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12867107	0.87[EUR][1000 genomes]
rs1335288	0.84[EUR][1000 genomes]
rs1414110	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2039554	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2039555	0.86[EUR][1000 genomes]
rs2039556	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2152226	0.85[EUR][1000 genomes]
rs2248409	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2248413	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248563	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2262460	0.88[EUR][1000 genomes]
rs2329137	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2329138	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2783085	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802634	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2802638	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2802640	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35661635	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4885658	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885660	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4885669	0.85[EUR][1000 genomes]
rs7322877	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7327527	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[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];0.83[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs915260	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9530958	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9530959	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9545191	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545203	0.86[EUR][1000 genomes]
rs9545205	0.86[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
rs2802641	HES2	trans	parietal	SCAN

Chromatin state (count:36 , 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	chr13:80315400-80324400	Weak transcription	Pancreas	Pancrea
4	chr13:80315400-80324400	Weak transcription	Small Intestine	intestine
5	chr13:80315800-80324600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr13:80317400-80324000	Weak transcription	NHEK	skin
7	chr13:80319200-80324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:80319600-80324000	Weak transcription	Fetal Stomach	stomach
9	chr13:80319600-80330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:80322800-80325200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr13:80322800-80325400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:80322800-80325800	Enhancers	Fetal Kidney	kidney
13	chr13:80323000-80324800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr13:80323000-80325200	Enhancers	Fetal Heart	heart
15	chr13:80323000-80325400	Enhancers	Fetal Muscle Leg	muscle
16	chr13:80323200-80324400	Weak transcription	Right Ventricle	heart
17	chr13:80323400-80324800	Enhancers	Psoas Muscle	Psoas
18	chr13:80323400-80325200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:80323400-80325400	Enhancers	HSMMtube	muscle
20	chr13:80323400-80325600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:80323600-80325000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr13:80323600-80325000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:80323600-80325200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:80323600-80325400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:80323600-80326200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:80323800-80324000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:80323800-80324600	Enhancers	Ovary	ovary
28	chr13:80323800-80324800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr13:80323800-80325000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:80323800-80325000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:80323800-80325000	Enhancers	Fetal Lung	lung
32	chr13:80323800-80325000	Enhancers	Osteobl	bone
33	chr13:80323800-80325200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:80323800-80325200	Enhancers	HMEC	breast
35	chr13:80323800-80325200	Enhancers	NHDF-Ad	bronchial
36	chr13:80323800-80325200	Enhancers	NHLF	lung

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