Variant report

Variant	rs8002574
Chromosome Location	chr13:40078540-40078541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1475175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1475176	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17807293	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1927196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3858866	1.00[ASN][1000 genomes]
rs4943668	1.00[ASN][1000 genomes]
rs4943669	1.00[ASN][1000 genomes]
rs4943670	1.00[ASN][1000 genomes]
rs4943671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55838454	0.98[ASN][1000 genomes]
rs56774016	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6563712	1.00[ASN][1000 genomes]
rs6563713	1.00[ASN][1000 genomes]
rs6563714	1.00[ASN][1000 genomes]
rs7139794	0.98[ASN][1000 genomes]
rs7317187	0.98[ASN][1000 genomes]
rs7321906	0.98[ASN][1000 genomes]
rs7322026	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7324077	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7335002	0.95[ASN][1000 genomes]
rs7335427	0.98[ASN][1000 genomes]
rs7335605	0.98[ASN][1000 genomes]
rs7981363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7982627	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8002691	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs912043	0.98[ASN][1000 genomes]
rs912044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9315691	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9315692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9548785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9576824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9594334	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9594335	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9594336	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9594337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9603549	1.00[ASN][1000 genomes]
rs9603550	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9603551	1.00[ASN][1000 genomes]
rs9603552	1.00[ASN][1000 genomes]
rs9603554	1.00[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757529	chr13:40040036-40090742	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759933	chr13:40040036-40090742	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8002574	NBEA	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40061600-40081000	Weak transcription	Osteobl	bone
2	chr13:40064800-40081200	Weak transcription	HSMMtube	muscle
3	chr13:40068400-40080800	Weak transcription	Fetal Brain Female	brain
4	chr13:40069200-40080400	Weak transcription	Aorta	Aorta
5	chr13:40073000-40081200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:40073800-40081200	Weak transcription	Esophagus	oesophagus
7	chr13:40073800-40084200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:40074200-40081000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:40074200-40094400	Weak transcription	Adipose Nuclei	Adipose
10	chr13:40074600-40080600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:40076200-40081000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:40076400-40079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:40076400-40079800	Weak transcription	Psoas Muscle	Psoas
14	chr13:40076400-40080400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:40076400-40080400	Weak transcription	Fetal Brain Male	brain
16	chr13:40076400-40080800	Weak transcription	Fetal Lung	lung
17	chr13:40076400-40081000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:40076400-40081000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:40076400-40081200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr13:40076400-40081200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:40076400-40081200	Weak transcription	Colon Smooth Muscle	Colon
22	chr13:40076400-40081200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:40076400-40081400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr13:40076400-40084000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr13:40076400-40084000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr13:40076400-40089000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr13:40076400-40096000	Weak transcription	Lung	lung
28	chr13:40076600-40079800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:40076600-40081200	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:40077200-40081000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:40077400-40079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:40077400-40081200	Weak transcription	Ovary	ovary
33	chr13:40077400-40088400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:40077400-40088400	Weak transcription	Right Atrium	heart
35	chr13:40077600-40079600	Weak transcription	Placenta	Placenta
36	chr13:40077600-40080400	Weak transcription	Left Ventricle	heart
37	chr13:40077600-40080600	Weak transcription	Right Ventricle	heart
38	chr13:40077600-40088400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:40077600-40101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:40077800-40079200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:40077800-40080400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr13:40078400-40078800	Weak transcription	Fetal Heart	heart

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