Variant report

Variant	rs39510
Chromosome Location	chr8:90804641-90804642
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90794527..90798218-chr8:90801291..90805045,3	K562	blood:
2	chr8:90800083..90802743-chr8:90803621..90807196,3	MCF-7	breast:
3	chr8:90801295..90805562-chr8:90810503..90814895,4	MCF-7	breast:
4	chr8:90767178..90772166-chr8:90803183..90807118,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251136	Chromatin interaction
ENSG00000104312	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10956243	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956244	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276910	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13282591	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160419	1.00[CHB][hapmap]
rs218898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs218904	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs218938	0.83[CHD][hapmap]
rs390993	1.00[LWK][hapmap];0.86[MKK][hapmap]
rs39502	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs39518	1.00[CHB][hapmap]
rs39760	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39765	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39770	0.88[CEU][hapmap]

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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs39510	CNGB3	cis	parietal	SCAN
rs39510	SLC26A7	cis	cerebellum	SCAN
rs39510	CALB1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90771800-90805000	Weak transcription	Esophagus	oesophagus
2	chr8:90772200-90805200	Weak transcription	Fetal Brain Male	brain
3	chr8:90772200-90807200	Weak transcription	Pancreas	Pancrea
4	chr8:90772200-90809400	Weak transcription	Small Intestine	intestine
5	chr8:90773000-90806800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:90773000-90812400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:90775800-90807200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:90781400-90806600	Weak transcription	Right Ventricle	heart
9	chr8:90781800-90805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
11	chr8:90785600-90813800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:90785800-90807200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:90785800-90810800	Weak transcription	Fetal Brain Female	brain
14	chr8:90786000-90813000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr8:90786400-90809800	Weak transcription	HepG2	liver
16	chr8:90792200-90805800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:90793600-90806400	Strong transcription	Liver	Liver
18	chr8:90795000-90805400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr8:90795000-90808400	Weak transcription	NHEK	skin
20	chr8:90795200-90805400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:90795600-90806400	Strong transcription	Adipose Nuclei	Adipose
22	chr8:90796200-90807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:90796600-90806400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr8:90797200-90808400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:90798000-90806200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr8:90798000-90806200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr8:90798000-90806400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr8:90798000-90806600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr8:90798400-90805600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr8:90798800-90805400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:90799400-90810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:90799400-90814000	Weak transcription	Gastric	stomach
33	chr8:90799800-90806600	Weak transcription	Ovary	ovary
34	chr8:90799800-90811800	Weak transcription	Fetal Kidney	kidney
35	chr8:90800000-90808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:90800800-90806400	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:90801000-90808000	Weak transcription	Fetal Stomach	stomach
38	chr8:90801000-90809600	Weak transcription	Fetal Intestine Small	intestine
39	chr8:90801200-90809800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:90801600-90806400	Strong transcription	Primary B cells from cord blood	blood
41	chr8:90802200-90805600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr8:90802400-90804800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr8:90802400-90805000	Weak transcription	GM12878-XiMat	blood
44	chr8:90802400-90806600	Weak transcription	Brain Angular Gyrus	brain
45	chr8:90802400-90806600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr8:90802400-90808000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:90802600-90805000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr8:90802600-90805000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:90802600-90805400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr8:90802600-90805400	Weak transcription	Left Ventricle	heart

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