Variant report

Variant	rs1323566
Chromosome Location	chr13:76451240-76451241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr13:76450142-76451486	SK-N-SH	brain:	n/a	chr13:76450712-76450726 chr13:76450402-76450412 chr13:76450398-76450412
2	RAD21	chr13:76450079-76451484	SK-N-SH	brain:	n/a	chr13:76450402-76450412 chr13:76450400-76450413 chr13:76451175-76451187 chr13:76450711-76450730
3	CTCF	chr13:76450152-76451245	SK-N-SH	brain:	n/a	chr13:76450399-76450412 chr13:76450713-76450722 chr13:76450712-76450733 chr13:76450396-76450409 chr13:76450710-76450728

Variant related genes	Relation type
ENSG00000223458	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1015694	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1036867	0.81[ASN][1000 genomes]
rs1036868	0.81[ASN][1000 genomes]
rs10507835	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1323565	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323567	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1399	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1550620	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2120066	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs35986631	0.85[EUR][1000 genomes]
rs4329801	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4418941	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4508318	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4572275	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4598784	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4884024	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4885358	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4885359	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885360	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885361	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885362	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6562923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7981821	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7986288	0.85[EUR][1000 genomes]
rs7986419	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7986876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7987971	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7995080	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9318381	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9530472	0.85[CEU][hapmap]
rs9530473	0.81[CEU][hapmap]
rs9530477	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9530479	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9530481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9530483	0.81[ASN][1000 genomes]
rs9530484	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9544058	0.93[YRI][hapmap]
rs9544060	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9544065	0.86[EUR][1000 genomes]
rs9544069	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9544071	0.81[ASN][1000 genomes]
rs9593137	0.99[ASN][1000 genomes]
rs9600572	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9600574	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9600575	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9600577	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9600578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9600579	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9600581	0.81[ASN][1000 genomes]
rs9600582	0.81[ASN][1000 genomes]
rs969394	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1323566	C13orf45	cis	Nerve Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76445400-76454400	Weak transcription	Osteobl	bone
3	chr13:76445600-76453400	Weak transcription	Adipose Nuclei	Adipose
4	chr13:76445600-76453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:76449000-76451600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr13:76449600-76451600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr13:76450200-76451800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:76450400-76451400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr13:76450400-76451400	Enhancers	Fetal Heart	heart
10	chr13:76450400-76451400	Enhancers	Fetal Lung	lung
11	chr13:76450400-76451400	Enhancers	A549	lung
12	chr13:76450400-76451600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:76450400-76451600	Enhancers	Fetal Muscle Leg	muscle
14	chr13:76450800-76451400	Enhancers	Fetal Kidney	kidney
15	chr13:76450800-76451400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr13:76450800-76451400	Enhancers	HSMMtube	muscle
17	chr13:76450800-76451600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr13:76450800-76451600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr13:76450800-76451600	Enhancers	Rectal Smooth Muscle	rectum
20	chr13:76450800-76451800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:76451000-76451400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr13:76451000-76451600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:76451000-76451600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:76451000-76451600	Enhancers	H9 Cell Line	embryonic stem cell
25	chr13:76451000-76451600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:76451000-76451800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:76451000-76452600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:76451200-76451400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:76451200-76451600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:76451200-76451600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:76451200-76452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:76451200-76453800	Weak transcription	Colon Smooth Muscle	Colon
33	chr13:76451200-76454000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:76451200-76454800	Weak transcription	Fetal Stomach	stomach

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