Variant report

Variant	rs3798752
Chromosome Location	chr6:11360163-11360164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11229074..11235774-chr6:11355894..11361748,7	MCF-7	breast:
2	chr6:11349169..11351708-chr6:11358591..11361451,2	K562	blood:
3	chr6:11344982..11346755-chr6:11356933..11360396,3	MCF-7	breast:
4	chr6:11358576..11361790-chr6:11363070..11366053,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1012502	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1013678	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10947204	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12199545	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12204242	0.90[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs12208626	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12215372	0.85[CHB][hapmap];0.83[GIH][hapmap]
rs12215715	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs13217274	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs2179178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4403261	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4711271	0.95[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4711272	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5019594	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6903648	0.83[YRI][hapmap]
rs6918440	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6932496	0.85[CHB][hapmap];0.83[GIH][hapmap]
rs6934773	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7738560	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7768351	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9296000	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9348868	0.95[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9357127	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9461714	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised 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	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3798752	MAK	cis	cerebellum	SCAN
rs3798752	C6orf218	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11355000-11364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:11355000-11367400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:11355200-11360400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:11355200-11361000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:11355200-11365200	Weak transcription	Left Ventricle	heart
6	chr6:11355200-11370800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:11357000-11360400	Enhancers	Placenta	Placenta
8	chr6:11357200-11362800	Enhancers	HepG2	liver
9	chr6:11357200-11371200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:11357600-11360800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr6:11357600-11362600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:11357600-11364200	Weak transcription	Right Atrium	heart
13	chr6:11357600-11365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:11357600-11367600	Weak transcription	Aorta	Aorta
15	chr6:11357800-11360200	Weak transcription	Fetal Thymus	thymus
16	chr6:11357800-11364600	Weak transcription	HUVEC	blood vessel
17	chr6:11357800-11365200	Weak transcription	Lung	lung
18	chr6:11357800-11366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:11357800-11370400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:11358000-11364400	Weak transcription	Spleen	Spleen
21	chr6:11358000-11367800	Weak transcription	Small Intestine	intestine
22	chr6:11358200-11360600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:11358200-11360800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:11358200-11367400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:11358600-11360600	Genic enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:11358600-11361000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:11358800-11360200	Enhancers	Adipose Nuclei	Adipose
28	chr6:11358800-11360600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:11358800-11366400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:11358800-11367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:11359000-11360200	Enhancers	HMEC	breast
32	chr6:11359000-11360800	Strong transcription	Primary B cells from cord blood	blood
33	chr6:11359000-11360800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:11359200-11360400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:11359400-11360200	Enhancers	NHEK	skin
36	chr6:11359400-11360400	Genic enhancers	Primary T cells from cord blood	blood
37	chr6:11359400-11361200	Strong transcription	Thymus	Thymus
38	chr6:11359400-11369800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:11359600-11364200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:11359600-11366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:11359800-11360600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:11359800-11360600	Weak transcription	Stomach Mucosa	stomach
43	chr6:11359800-11364000	ZNF genes & repeats	GM12878-XiMat	blood
44	chr6:11360000-11360200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr6:11360000-11360200	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:11360000-11360200	Enhancers	Right Ventricle	heart
47	chr6:11360000-11360600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:11360000-11360800	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr6:11360000-11360800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:11360000-11361000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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