Variant report

Variant	rs428484
Chromosome Location	chr8:90776033-90776034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90774651..90777545-chr8:90807253..90809374,2	MCF-7	breast:
2	chr8:90775245..90777466-chr8:90780625..90782442,2	K562	blood:
3	chr8:90775597..90777487-chr8:90778142..90780568,2	K562	blood:
4	chr8:90774118..90777411-chr8:90913721..90915849,3	MCF-7	breast:
5	chr8:90775966..90778463-chr8:90780267..90782442,2	K562	blood:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11776336	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11995005	0.85[CHD][hapmap]
rs12156013	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13254219	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13274635	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16900429	0.84[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap]
rs218935	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs218938	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs370282	0.85[CEU][hapmap]
rs383592	0.92[CEU][hapmap]
rs39501	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39502	0.89[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39508	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39509	0.92[CEU][hapmap]
rs39511	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39512	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs397540	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs39762	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs39763	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39766	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs398701	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40247	0.89[CEU][hapmap]
rs40248	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40378	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40379	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40380	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40453	0.88[CEU][hapmap]
rs40454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40547	0.85[CEU][hapmap]
rs40635	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40638	0.85[CEU][hapmap]
rs406680	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs411279	0.89[CEU][hapmap]
rs411310	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs416324	0.92[CEU][hapmap]
rs42343	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs42346	0.85[CEU][hapmap]
rs42479	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs42480	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]
rs425721	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426779	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43133	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434264	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs450332	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs428484	CNGB3	cis	parietal	SCAN
rs428484	CALB1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90771000-90797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:90771600-90803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:90771800-90777400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:90771800-90784400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:90771800-90805000	Weak transcription	Esophagus	oesophagus
6	chr8:90772000-90776200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr8:90772000-90777400	Weak transcription	Primary T cells from cord blood	blood
8	chr8:90772000-90778000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr8:90772000-90778400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:90772000-90784600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr8:90772000-90785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:90772000-90785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:90772000-90796800	Weak transcription	Lung	lung
14	chr8:90772000-90797000	Weak transcription	Ovary	ovary
15	chr8:90772200-90777600	Weak transcription	Placenta	Placenta
16	chr8:90772200-90778000	Weak transcription	Fetal Kidney	kidney
17	chr8:90772200-90778200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr8:90772200-90778200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:90772200-90778200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr8:90772200-90783600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr8:90772200-90783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:90772200-90784600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr8:90772200-90785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:90772200-90785600	Weak transcription	Fetal Muscle Leg	muscle
25	chr8:90772200-90802000	Weak transcription	Colonic Mucosa	Colon
26	chr8:90772200-90802400	Weak transcription	Spleen	Spleen
27	chr8:90772200-90805200	Weak transcription	Fetal Brain Male	brain
28	chr8:90772200-90807200	Weak transcription	Pancreas	Pancrea
29	chr8:90772200-90809400	Weak transcription	Small Intestine	intestine
30	chr8:90772400-90777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:90772400-90777600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr8:90772400-90778200	Weak transcription	Fetal Intestine Large	intestine
33	chr8:90772400-90778200	Weak transcription	Fetal Lung	lung
34	chr8:90772400-90784000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:90772400-90784600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr8:90772400-90784800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr8:90772400-90784800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr8:90772400-90785200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:90772400-90787200	Weak transcription	Fetal Stomach	stomach
40	chr8:90772400-90790600	Weak transcription	NHEK	skin
41	chr8:90772400-90802200	Weak transcription	Colon Smooth Muscle	Colon
42	chr8:90772600-90776200	Weak transcription	Brain Hippocampus Middle	brain
43	chr8:90772600-90777800	Weak transcription	Liver	Liver
44	chr8:90772600-90784400	Weak transcription	Left Ventricle	heart
45	chr8:90773000-90776400	Weak transcription	Primary B cells from cord blood	blood
46	chr8:90773000-90783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr8:90773000-90784400	Weak transcription	HSMMtube	muscle
48	chr8:90773000-90785200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:90773000-90785200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr8:90773000-90806800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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