Variant report

Variant	rs9805226
Chromosome Location	chr13:95676644-95676645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11568662	1.00[AMR][1000 genomes]
rs73544903	1.00[AMR][1000 genomes]
rs73561745	1.00[AMR][1000 genomes]
rs74105420	1.00[AMR][1000 genomes]
rs74107809	1.00[AMR][1000 genomes]
rs74107814	1.00[AMR][1000 genomes]
rs74107818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74107819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9524766	0.84[AFR][1000 genomes]
rs9590144	1.00[AMR][1000 genomes]
rs9590156	1.00[AMR][1000 genomes]
rs9590161	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9590163	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv832688	chr13:95633193-95780198	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv525194	chr13:95672950-95737192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv3427279	chr13:95676351-95678649	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9805226	SYCE1	trans	lymphoblastoid	seeQTL
rs9805226	TSPAN1	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95655600-95722600	Weak transcription	Gastric	stomach
2	chr13:95661400-95694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:95666800-95681800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:95668600-95712000	Weak transcription	NHDF-Ad	bronchial
5	chr13:95669000-95680000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:95669000-95686400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:95669400-95686000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:95669400-95690800	Weak transcription	Ovary	ovary
9	chr13:95669400-95723200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:95669600-95686200	Weak transcription	NHLF	lung
11	chr13:95669600-95692000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr13:95669600-95744000	Weak transcription	Small Intestine	intestine
13	chr13:95670000-95690600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr13:95670200-95677400	Weak transcription	HSMM	muscle
15	chr13:95671400-95690800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr13:95671400-95690800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:95671400-95722200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:95671600-95688600	Weak transcription	Right Ventricle	heart
19	chr13:95671600-95692200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:95672600-95686600	Weak transcription	A549	lung
21	chr13:95672800-95729000	Weak transcription	Colonic Mucosa	Colon
22	chr13:95673000-95688600	Weak transcription	HSMMtube	muscle
23	chr13:95673200-95677400	Weak transcription	K562	blood
24	chr13:95673200-95693200	Weak transcription	Primary T cells from cord blood	blood
25	chr13:95673400-95678000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:95673400-95680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:95673600-95686600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr13:95673600-95690800	Weak transcription	GM12878-XiMat	blood
29	chr13:95673800-95690400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr13:95674600-95690800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr13:95675400-95693600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr13:95675600-95677000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:95675600-95677400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:95676000-95677200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:95676000-95677400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr13:95676000-95677400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr13:95676000-95740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:95676400-95676800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr13:95676400-95677400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:95676600-95677000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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