Variant report

Variant	rs6909620
Chromosome Location	chr6:30448668-30448669
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30447797..30449612-chr6:30512660..30515323,2	MCF-7	breast:
2	chr6:30448465..30450230-chr6:30522710..30525074,2	K562	blood:
3	chr6:30446309..30448997-chr6:30451629..30454419,2	MCF-7	breast:
4	chr6:30447631..30450065-chr6:30691817..30695001,3	K562	blood:
5	chr6:30422351..30425241-chr6:30448232..30450888,2	MCF-7	breast:
6	chr6:30446384..30451689-chr6:30578094..30585004,12	MCF-7	breast:
7	chr6:30447476..30449412-chr6:30509865..30511998,2	K562	blood:
8	chr6:30448170..30453321-chr6:30582822..30586539,6	K562	blood:
9	chr6:30447949..30451648-chr6:30569801..30572499,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204590	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000236603	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11963959	0.83[AFR][1000 genomes]
rs11968857	0.80[AFR][1000 genomes]
rs16897572	0.88[ASN][1000 genomes]
rs17411284	0.82[AFR][1000 genomes]
rs17411410	0.82[AFR][1000 genomes]
rs17411480	0.82[AFR][1000 genomes]
rs2428536	0.81[AFR][1000 genomes]
rs34101875	0.82[AFR][1000 genomes]
rs34163258	0.82[AFR][1000 genomes]
rs34186179	0.83[AFR][1000 genomes]
rs34335619	0.81[AFR][1000 genomes]
rs34340584	0.82[AFR][1000 genomes]
rs34435337	0.82[AFR][1000 genomes]
rs34552114	0.83[AFR][1000 genomes]
rs34708826	0.83[AFR][1000 genomes]
rs34762601	0.82[AFR][1000 genomes]
rs34960122	0.83[AFR][1000 genomes]
rs35227387	0.82[AFR][1000 genomes]
rs35230915	0.82[AFR][1000 genomes]
rs35268644	0.82[AFR][1000 genomes]
rs35365548	0.82[AFR][1000 genomes]
rs35407515	0.82[AFR][1000 genomes]
rs35698032	0.82[AFR][1000 genomes]
rs35792611	0.87[AFR][1000 genomes]
rs36034295	0.83[AFR][1000 genomes]
rs36093514	0.83[AFR][1000 genomes]
rs41265603	0.82[AFR][1000 genomes]
rs6902129	0.83[AFR][1000 genomes]
rs6902374	0.83[AFR][1000 genomes]
rs6902914	0.83[AFR][1000 genomes]
rs6924512	0.83[AFR][1000 genomes]
rs9295872	0.82[AFR][1000 genomes]
rs9295874	0.82[AFR][1000 genomes]
rs9295887	0.82[AFR][1000 genomes]
rs9295888	0.82[AFR][1000 genomes]
rs9295893	0.83[AFR][1000 genomes]
rs9295894	0.83[AFR][1000 genomes]
rs9461608	0.82[AFR][1000 genomes]
rs9461609	0.82[AFR][1000 genomes]
rs9461611	0.83[AFR][1000 genomes]
rs9468759	0.81[AFR][1000 genomes]
rs9468760	0.81[AFR][1000 genomes]
rs9468768	0.82[AFR][1000 genomes]
rs9468773	0.82[AFR][1000 genomes]
rs9468774	0.82[AFR][1000 genomes]
rs9468780	0.87[AFR][1000 genomes]
rs9468781	0.86[AFR][1000 genomes]
rs9501020	0.82[AFR][1000 genomes]
rs9501328	0.82[AFR][1000 genomes]
rs9501329	0.83[AFR][1000 genomes]
rs9501335	0.83[AFR][1000 genomes]
rs9501336	0.83[AFR][1000 genomes]
rs9501471	0.82[AFR][1000 genomes]
rs9501474	0.83[AFR][1000 genomes]
rs9885617	0.82[AFR][1000 genomes]
rs9885618	0.82[AFR][1000 genomes]
rs9885620	0.82[AFR][1000 genomes]
rs9885622	0.82[AFR][1000 genomes]
rs9885685	0.82[AFR][1000 genomes]
rs9885815	0.82[AFR][1000 genomes]
rs9918350	0.82[AFR][1000 genomes]
rs9918488	0.82[AFR][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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884069	chr6:30430875-30451474	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv884070	chr6:30430875-30472772	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
7	nsv884075	chr6:30434566-30449046	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6909620	C6orf106	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30447800-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:30448000-30449800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
3	chr6:30448000-30450000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
4	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr6:30448000-30450200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:30448200-30448800	Bivalent Enhancer	Primary T cells from cord blood	blood
8	chr6:30448200-30448800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
9	chr6:30448200-30448800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:30448200-30448800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:30448200-30449000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr6:30448200-30449200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr6:30448200-30449200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:30448200-30449200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr6:30448200-30449200	Flanking Bivalent TSS/Enh	NHEK	skin
16	chr6:30448200-30449600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
17	chr6:30448200-30450000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
20	chr6:30448200-30450000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
21	chr6:30448200-30450000	Bivalent Enhancer	Fetal Thymus	thymus
22	chr6:30448200-30450000	Bivalent Enhancer	GM12878-XiMat	blood
23	chr6:30448200-30450200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:30448200-30450400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr6:30448400-30448800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr6:30448400-30448800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:30448400-30448800	Bivalent Enhancer	Dnd41	blood
28	chr6:30448400-30449000	Bivalent Enhancer	HepG2	liver
29	chr6:30448400-30449600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:30448400-30449800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
31	chr6:30448400-30449800	Bivalent Enhancer	HUVEC	blood vessel
32	chr6:30448400-30450000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:30448400-30450000	Bivalent Enhancer	Primary B cells from cord blood	blood
34	chr6:30448400-30450000	Enhancers	Spleen	Spleen
35	chr6:30448400-30450000	Bivalent Enhancer	HMEC	breast
36	chr6:30448400-30450400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr6:30448600-30448800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
38	chr6:30448600-30448800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr6:30448600-30448800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
40	chr6:30448600-30448800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:30448600-30448800	Flanking Bivalent TSS/Enh	A549	lung
42	chr6:30448600-30448800	Bivalent Enhancer	K562	blood
43	chr6:30448600-30449000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:30448600-30449000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:30448600-30449000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:30448600-30449000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:30448600-30449400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:30448600-30449600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:30448600-30449600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:30448600-30449800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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