Variant report

Variant	rs2008239
Chromosome Location	chr3:69406469-69406470
allele	C/T
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	CEBPB	chr3:69406405-69406753	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11128125	1.00[ASW][hapmap];0.89[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1564758	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2005546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34397489	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549200	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs6549204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6549213	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs6763080	0.94[ASN][1000 genomes]
rs6774290	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6781841	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802833	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6808107	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610748	0.86[ASN][1000 genomes]
rs7615137	0.82[ASN][1000 genomes]
rs7640281	0.91[ASN][1000 genomes]
rs9820308	0.92[CHD][hapmap];0.84[LWK][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs9820322	0.86[ASN][1000 genomes]
rs9867072	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869925	1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9876410	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs9882259	0.85[AFR][1000 genomes];0.87[ASN][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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008239	EBLN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
2	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:69402800-69413000	Weak transcription	Aorta	Aorta
4	chr3:69403000-69414800	Weak transcription	Lung	lung
5	chr3:69403800-69406600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:69403800-69413000	Weak transcription	Thymus	Thymus
7	chr3:69404200-69408200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:69404600-69407000	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:69405000-69408600	Weak transcription	HUVEC	blood vessel
10	chr3:69405800-69406800	Enhancers	Brain Substantia Nigra	brain
11	chr3:69406000-69406600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:69406000-69406800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:69406000-69407000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:69406000-69407200	Enhancers	Hela-S3	cervix
15	chr3:69406000-69407200	Genic enhancers	NHEK	skin
16	chr3:69406000-69407400	Enhancers	HSMMtube	muscle
17	chr3:69406000-69407600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:69406000-69407600	Enhancers	HMEC	breast
19	chr3:69406200-69406600	Enhancers	Fetal Thymus	thymus
20	chr3:69406200-69406600	Enhancers	Left Ventricle	heart
21	chr3:69406200-69406600	Enhancers	Right Atrium	heart
22	chr3:69406200-69406800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:69406200-69406800	Enhancers	Dnd41	blood
24	chr3:69406200-69407200	Enhancers	Brain Anterior Caudate	brain
25	chr3:69406200-69407400	Enhancers	Brain Hippocampus Middle	brain
26	chr3:69406200-69407600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:69406200-69407600	Enhancers	Fetal Lung	lung
28	chr3:69406200-69408000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:69406200-69408000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:69406400-69406800	Enhancers	Brain Angular Gyrus	brain
31	chr3:69406400-69406800	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:69406400-69406800	Weak transcription	HSMM	muscle
33	chr3:69406400-69406800	Enhancers	NHLF	lung
34	chr3:69406400-69407400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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