Variant report

Variant	rs2683280
Chromosome Location	chr8:19129368-19129369
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19128887..19134305-chr8:19169094..19173373,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104611	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10088667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10091480	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10091481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10105631	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10108694	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204027	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11779774	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1193287	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs1193288	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1193290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193291	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193293	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1193296	0.83[ASN][1000 genomes]
rs1193297	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1193305	0.89[ASN][1000 genomes]
rs1193308	0.81[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1193309	0.89[ASN][1000 genomes]
rs13261970	0.81[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1473939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1473940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1514702	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1514704	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915404	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1915406	0.87[ASN][1000 genomes]
rs1915407	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915408	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967513	0.84[EUR][1000 genomes]
rs2139762	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2139763	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176925	0.80[EUR][1000 genomes]
rs2244965	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2672262	0.83[JPT][hapmap]
rs2683279	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683285	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2683314	0.83[JPT][hapmap]
rs2683319	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2943426	0.83[ASN][1000 genomes]
rs2943427	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2947260	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2947261	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2947262	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2947263	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34123475	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34192188	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34254629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34265536	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34267592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34694243	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35604334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35651150	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36039247	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4922006	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922007	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55811677	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55846624	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6586822	0.89[ASN][1000 genomes]
rs6586823	0.90[ASN][1000 genomes]
rs7814080	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7841513	0.90[ASN][1000 genomes]
rs871667	0.83[CHB][hapmap]
rs871668	0.87[CHB][hapmap]
rs991589	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv917232	chr8:18585309-19208665	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv890615	chr8:18989735-19181921	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv890616	chr8:18989735-19197809	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv1033297	chr8:19108472-19150023	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1034119	chr8:19115084-19164833	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv465599	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv610747	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv465600	chr8:19116030-19156100	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv610748	chr8:19116030-19156100	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv610749	chr8:19116030-19160915	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv470202	chr8:19128303-19168142	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv610750	chr8:19128303-19168142	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2683280	NAT2	cis	cerebellum	SCAN
rs2683280	ZXDB	trans	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19121600-19129400	Weak transcription	Spleen	Spleen
2	chr8:19122400-19129800	Weak transcription	Pancreas	Pancrea
3	chr8:19123200-19129800	Weak transcription	Gastric	stomach
4	chr8:19125600-19129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:19125600-19129400	Weak transcription	NHEK	skin
6	chr8:19125600-19131200	Weak transcription	Fetal Heart	heart
7	chr8:19125600-19131200	Weak transcription	Right Atrium	heart
8	chr8:19125600-19131400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:19125800-19131000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:19125800-19131000	Weak transcription	Fetal Lung	lung
11	chr8:19125800-19131200	Weak transcription	Adipose Nuclei	Adipose
12	chr8:19126000-19129400	Weak transcription	Stomach Mucosa	stomach
13	chr8:19126000-19129400	Weak transcription	Hela-S3	cervix
14	chr8:19126000-19131200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:19127800-19133400	Enhancers	Liver	Liver
16	chr8:19128800-19130000	Enhancers	HMEC	breast
17	chr8:19128800-19130400	Enhancers	A549	lung
18	chr8:19129200-19129600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr8:19129200-19129800	Enhancers	HepG2	liver
20	chr8:19129200-19130000	Enhancers	Primary hematopoietic stem cells	blood
21	chr8:19129200-19130000	Enhancers	HUVEC	blood vessel

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