Variant report

Variant	rs3800130
Chromosome Location	chr6:1918122-1918123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1608029..1610545-chr6:1915416..1919377,4	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12173320	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12175531	0.87[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1323631	0.87[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146920	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800143	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3927456	0.87[EUR][1000 genomes]
rs6900111	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939971	0.90[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9405154	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405155	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405533	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800130	NQO2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1901600-1923400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
3	chr6:1905200-1926000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:1905200-1926000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
6	chr6:1908000-1919800	Weak transcription	GM12878-XiMat	blood
7	chr6:1908400-1933600	Weak transcription	Liver	Liver
8	chr6:1909800-1926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
10	chr6:1913000-1918600	Enhancers	Dnd41	blood
11	chr6:1914800-1930800	Strong transcription	HepG2	liver
12	chr6:1915000-1918200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr6:1915200-1934000	Weak transcription	Left Ventricle	heart
14	chr6:1915200-1937600	Weak transcription	Esophagus	oesophagus
15	chr6:1915800-1923400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:1915800-1923400	Weak transcription	Fetal Stomach	stomach
17	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
18	chr6:1916000-1918600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:1916000-1928600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:1916000-1960800	Weak transcription	Gastric	stomach
21	chr6:1916200-1918200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:1916200-1918200	Enhancers	HSMMtube	muscle
23	chr6:1916200-1918200	Enhancers	NHDF-Ad	bronchial
24	chr6:1916200-1918600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:1916200-1918800	Enhancers	HMEC	breast
26	chr6:1916200-1930000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:1916400-1918600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:1916400-1918600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:1916400-1918800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:1916400-1919000	Enhancers	NHEK	skin
31	chr6:1916400-1919200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:1916400-1920000	Weak transcription	Primary T cells from cord blood	blood
33	chr6:1916600-1918600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:1916600-1918600	Enhancers	Hela-S3	cervix
35	chr6:1916600-1918600	Enhancers	HSMM	muscle
36	chr6:1916600-1919000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:1916600-1926200	Weak transcription	Fetal Intestine Small	intestine
38	chr6:1916600-1935000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:1916800-1918200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:1916800-1918200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:1916800-1918600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:1916800-1918600	Enhancers	NH-A	brain
43	chr6:1917000-1918600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:1917000-1919000	Enhancers	HUVEC	blood vessel
45	chr6:1917000-1920400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:1917000-1926000	Weak transcription	Thymus	Thymus
47	chr6:1917200-1918600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr6:1917200-1918800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:1917400-1918200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:1917400-1920200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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