Variant report

Variant	rs9462082
Chromosome Location	chr6:35386041-35386042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35310293..35313222-chr6:35385909..35387818,2	MCF-7	breast:
2	chr6:35384923..35387386-chr6:35435041..35437575,2	MCF-7	breast:
3	chr6:35310404..35313411-chr6:35381684..35386621,4	MCF-7	breast:
4	chr6:35379744..35382549-chr6:35384456..35386159,2	K562	blood:
5	chr1:35658635..35659143-chr6:35386008..35386508,2	Hela-S3	cervix:
6	chr6:35374653..35376818-chr6:35385902..35387934,2	K562	blood:
7	chr6:35385294..35388987-chr6:35389022..35393579,4	K562	blood:
8	chr6:35328136..35331103-chr6:35385311..35387478,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction
ENSG00000116560	Chromatin interaction
ENSG00000112033	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1040436	0.86[CHD][hapmap]
rs1053049	0.86[CHD][hapmap]
rs1883322	0.88[CHD][hapmap]
rs2016520	0.93[CHD][hapmap]
rs2038067	0.87[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2038068	0.88[CHD][hapmap]
rs2076166	0.94[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076167	0.91[CHD][hapmap]
rs2076169	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2267665	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267666	0.88[CHD][hapmap]
rs2267667	0.88[CHD][hapmap]
rs2267668	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267669	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395622	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2894401	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs3734254	0.85[CHD][hapmap]
rs4713858	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6457819	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6899536	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs760783	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749160	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7749165	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7751481	0.88[CHD][hapmap]
rs9380506	0.87[ASN][1000 genomes]
rs9470015	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470020	0.81[ASN][1000 genomes]
rs9470024	0.90[ASN][1000 genomes]
rs9794	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9462082	C6orf106	cis	cerebellum	SCAN
rs9462082	C6orf81	cis	parietal	SCAN
rs9462082	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:35370600-35393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:35375600-35387000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:35377800-35395000	Weak transcription	K562	blood
5	chr6:35378000-35386400	Strong transcription	Spleen	Spleen
6	chr6:35378400-35386800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:35378800-35393400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:35379600-35386400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr6:35379800-35392600	Strong transcription	NHEK	skin
10	chr6:35380000-35386600	Strong transcription	Primary B cells from cord blood	blood
11	chr6:35380400-35392200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:35380400-35392200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:35380600-35387200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:35380600-35387600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:35381000-35389400	Weak transcription	HMEC	breast
16	chr6:35381200-35389600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:35381400-35386400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:35381400-35386800	Weak transcription	GM12878-XiMat	blood
19	chr6:35382800-35386600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:35382800-35390000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:35383000-35386600	Weak transcription	Fetal Lung	lung
22	chr6:35383000-35386600	Weak transcription	Left Ventricle	heart
23	chr6:35383000-35386800	Strong transcription	HSMM	muscle
24	chr6:35383000-35394600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:35383000-35396800	Weak transcription	Right Atrium	heart
26	chr6:35383200-35386200	Strong transcription	Placenta	Placenta
27	chr6:35383200-35386600	Strong transcription	Fetal Muscle Leg	muscle
28	chr6:35383200-35386800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:35383200-35387200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:35383200-35388600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:35383400-35386600	Strong transcription	Fetal Stomach	stomach
32	chr6:35383400-35387000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:35383400-35387200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:35383400-35389400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:35383400-35389600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:35383400-35394800	Weak transcription	Fetal Kidney	kidney
37	chr6:35383400-35396600	Weak transcription	Stomach Mucosa	stomach
38	chr6:35383600-35387400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:35383600-35389600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:35383600-35389600	Weak transcription	Colon Smooth Muscle	Colon
41	chr6:35383600-35392000	Weak transcription	Brain Germinal Matrix	brain
42	chr6:35383600-35402600	Weak transcription	Fetal Heart	heart
43	chr6:35383800-35386200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:35383800-35386600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr6:35383800-35386800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:35383800-35389400	Weak transcription	Fetal Brain Female	brain
47	chr6:35383800-35390600	Weak transcription	A549	lung
48	chr6:35383800-35391600	Weak transcription	Fetal Brain Male	brain
49	chr6:35384000-35386200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:35384000-35386800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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