Variant report

Variant	rs218904
Chromosome Location	chr8:90734506-90734507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90732834..90736227-chr8:90736670..90741646,5	MCF-7	breast:
2	chr8:90728791..90734507-chr8:90768671..90772991,6	MCF-7	breast:
3	chr8:90733158..90736113-chr8:90768378..90769934,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NBN-1	chr8:90734243-90734578	ENSG00000251136
2	lnc-NBN-1	chr8:90734243-90734578	NONHSAT127622

Variant related genes	Relation type
ENSG00000251136	Chromatin interaction
ENSG00000104312	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10956226	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10956243	0.86[ASN][1000 genomes]
rs10956244	0.86[ASN][1000 genomes]
rs13276910	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs13282591	0.86[ASN][1000 genomes]
rs1603288	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs160409	0.80[AMR][1000 genomes]
rs160410	0.80[AMR][1000 genomes]
rs160418	0.80[AMR][1000 genomes]
rs160419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs160445	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs160447	0.81[EUR][1000 genomes]
rs183363	0.82[EUR][1000 genomes]
rs2088198	0.81[EUR][1000 genomes]
rs2132348	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs216986	0.80[AMR][1000 genomes]
rs216990	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218892	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs218896	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218898	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs218915	0.83[EUR][1000 genomes]
rs218918	0.83[EUR][1000 genomes]
rs218920	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs218938	0.83[CHD][hapmap]
rs218943	0.88[EUR][1000 genomes]
rs218945	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218949	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs218950	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs218952	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2735886	0.80[AMR][1000 genomes]
rs28819479	0.84[EUR][1000 genomes]
rs39502	0.83[CHD][hapmap]
rs39510	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs39518	1.00[CHB][hapmap]
rs39760	0.86[ASN][1000 genomes]
rs39764	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs39765	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs419004	0.86[EUR][1000 genomes]
rs4961159	0.84[EUR][1000 genomes]
rs6999425	0.85[EUR][1000 genomes]
rs7828553	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1031578	chr8:90670102-90757821	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv6294	chr8:90705780-90750101	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs218904	CNGB3	cis	parietal	SCAN
rs218904	MMP16	cis	cerebellum	SCAN
rs218904	RIPK2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90710200-90736200	Weak transcription	Adipose Nuclei	Adipose
2	chr8:90713200-90741200	Weak transcription	Left Ventricle	heart
3	chr8:90713400-90738000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:90713600-90756200	Weak transcription	Pancreas	Pancrea
5	chr8:90714200-90741400	Weak transcription	Right Ventricle	heart
6	chr8:90714400-90741000	Weak transcription	Gastric	stomach
7	chr8:90715400-90741200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr8:90716800-90738000	Weak transcription	Brain Hippocampus Middle	brain
9	chr8:90717200-90741000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:90717400-90738000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:90717800-90736200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr8:90717800-90737800	Weak transcription	NHEK	skin
13	chr8:90717800-90738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:90717800-90738000	Weak transcription	NH-A	brain
15	chr8:90717800-90747800	Weak transcription	Ovary	ovary
16	chr8:90720800-90736000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:90720800-90742400	Weak transcription	Fetal Lung	lung
18	chr8:90721000-90740000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr8:90721200-90736400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:90721400-90735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:90721400-90740400	Weak transcription	Fetal Intestine Large	intestine
22	chr8:90721800-90738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr8:90725200-90736200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:90725200-90740400	Weak transcription	Small Intestine	intestine
25	chr8:90726600-90741400	Weak transcription	Esophagus	oesophagus
26	chr8:90726800-90738200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr8:90728400-90738000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:90729200-90737800	Weak transcription	Fetal Heart	heart
29	chr8:90730200-90737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:90731000-90738200	Weak transcription	K562	blood
31	chr8:90731000-90738400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:90731400-90736400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr8:90731400-90736400	Weak transcription	Colon Smooth Muscle	Colon
34	chr8:90731600-90736000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr8:90731600-90736200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr8:90731600-90736200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr8:90731600-90736400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr8:90731600-90736400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr8:90731800-90737000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr8:90731800-90738000	Weak transcription	NHLF	lung
41	chr8:90731800-90738600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr8:90732000-90737800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr8:90732000-90737800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr8:90732000-90737800	Weak transcription	NHDF-Ad	bronchial
45	chr8:90732000-90738200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:90732200-90738200	Weak transcription	HSMMtube	muscle
47	chr8:90732200-90738400	Weak transcription	HSMM	muscle
48	chr8:90732600-90736400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr8:90733200-90738000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr8:90733600-90736400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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