Variant report

Variant	rs10493761
Chromosome Location	chr1:85611277-85611278
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10873690	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161539	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12116526	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2168870	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907139	0.81[GIH][hapmap]
rs7366766	0.83[EUR][1000 genomes]
rs7531640	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10493761	SYDE2	cis	parietal	SCAN
rs10493761	C1orf52	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85594800-85614400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:85603800-85614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:85603800-85615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:85603800-85618800	Weak transcription	Gastric	stomach
5	chr1:85603800-85632200	Weak transcription	Fetal Lung	lung
6	chr1:85604800-85611800	Weak transcription	Placenta	Placenta
7	chr1:85608600-85614200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
9	chr1:85608800-85629200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:85609200-85614200	Weak transcription	Left Ventricle	heart
11	chr1:85609400-85611400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:85609800-85611400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:85610200-85611400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:85610200-85611400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:85610200-85611600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85610400-85611400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:85610400-85613800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:85610400-85614200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:85610400-85615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:85610600-85613800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:85610600-85613800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:85610600-85630600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:85610800-85611400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:85610800-85611400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:85611200-85611400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:85611200-85613800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:85611200-85615200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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