Variant report

Variant	rs42480
Chromosome Location	chr8:90812515-90812516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90811959..90814919-chr8:90863666..90865460,3	MCF-7	breast:
2	chr8:90788397..90791255-chr8:90811983..90814369,2	MCF-7	breast:
3	chr8:90810688..90812516-chr8:90813829..90816588,2	MCF-7	breast:
4	chr8:90769811..90771735-chr8:90809969..90812627,2	MCF-7	breast:
5	chr8:90801295..90805562-chr8:90810503..90814895,4	MCF-7	breast:
6	chr8:90810531..90814020-chr8:90816566..90819944,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104312	Chromatin interaction
ENSG00000251136	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10956271	0.82[CHB][hapmap]
rs11776336	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11995005	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12156013	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13254219	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13274635	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16893139	0.82[CHB][hapmap]
rs218935	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs218938	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293808	0.82[CHB][hapmap]
rs2293809	0.82[CHB][hapmap]
rs370282	0.85[CEU][hapmap]
rs383592	0.92[CEU][hapmap]
rs39501	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39502	0.89[CEU][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39508	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39509	0.92[CEU][hapmap]
rs39511	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39512	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39762	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs39766	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398701	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40247	0.89[CEU][hapmap]
rs40248	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40378	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40453	0.89[CEU][hapmap]
rs40454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40547	0.85[CEU][hapmap]
rs40635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40638	0.85[CEU][hapmap]
rs406680	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411279	0.89[CEU][hapmap]
rs411310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416324	0.92[CEU][hapmap]
rs42343	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs42346	0.85[CEU][hapmap]
rs42479	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs425721	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs426779	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs428484	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs43133	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs434264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs51331	0.92[CEU][hapmap]
rs7815039	0.88[AMR][1000 genomes];0.93[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs42480	CNGB3	cis	parietal	SCAN
rs42480	CALB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
2	chr8:90785600-90813800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:90786000-90813000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:90799400-90814000	Weak transcription	Gastric	stomach
5	chr8:90802600-90814200	Weak transcription	K562	blood
6	chr8:90803000-90813400	Weak transcription	Hela-S3	cervix
7	chr8:90803600-90813800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:90805400-90817000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:90806200-90814000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr8:90806400-90814000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr8:90807000-90812600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:90808000-90814000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:90808800-90813800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:90809800-90813400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:90810000-90813000	Weak transcription	NHEK	skin
16	chr8:90810000-90813200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr8:90810000-90813400	Weak transcription	NH-A	brain
18	chr8:90810000-90813800	Weak transcription	HSMM	muscle
19	chr8:90810200-90813400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:90810200-90813800	Enhancers	Placenta	Placenta
21	chr8:90810200-90814400	Enhancers	Fetal Intestine Large	intestine
22	chr8:90810400-90812600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr8:90810400-90813000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:90810400-90813000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr8:90810400-90813000	Weak transcription	NHLF	lung
26	chr8:90810400-90817000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:90810600-90813200	Weak transcription	HMEC	breast
28	chr8:90810600-90813400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr8:90810800-90812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:90811000-90813000	Weak transcription	Fetal Intestine Small	intestine
31	chr8:90811400-90812800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:90811400-90813200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr8:90812000-90813000	Weak transcription	Liver	Liver
34	chr8:90812000-90813200	Weak transcription	Stomach Mucosa	stomach
35	chr8:90812000-90813200	Weak transcription	Osteobl	bone
36	chr8:90812000-90813600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:90812000-90813800	Weak transcription	NHDF-Ad	bronchial
38	chr8:90812200-90813200	Enhancers	HepG2	liver
39	chr8:90812200-90813400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr8:90812400-90813000	Enhancers	A549	lung

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