Variant report

Variant	rs56899462
Chromosome Location	chr6:121566758-121566759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10499102	0.91[AFR][1000 genomes]
rs10499103	0.91[AFR][1000 genomes]
rs10499108	0.83[AFR][1000 genomes]
rs17083356	0.83[AFR][1000 genomes]
rs17083360	0.83[AFR][1000 genomes]
rs17083375	0.83[AFR][1000 genomes]
rs17083625	1.00[EUR][1000 genomes]
rs3923664	0.83[AFR][1000 genomes]
rs4441982	0.91[AFR][1000 genomes]
rs4469335	0.91[AFR][1000 genomes]
rs4585597	0.83[AFR][1000 genomes]
rs4945683	0.83[AFR][1000 genomes]
rs4946552	0.95[AFR][1000 genomes]
rs4946553	0.95[AFR][1000 genomes]
rs4946554	0.95[AFR][1000 genomes]
rs4946555	0.91[AFR][1000 genomes]
rs4946556	0.91[AFR][1000 genomes]
rs4946557	0.91[AFR][1000 genomes]
rs4946558	0.84[AFR][1000 genomes]
rs4946560	0.83[AFR][1000 genomes]
rs4946561	0.83[AFR][1000 genomes]
rs56721079	1.00[EUR][1000 genomes]
rs56758178	1.00[EUR][1000 genomes]
rs59863462	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59945135	0.91[AFR][1000 genomes]
rs60820338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61550917	0.83[AFR][1000 genomes]
rs61582983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901295	1.00[EUR][1000 genomes]
rs7766943	1.00[AMR][1000 genomes]
rs9482164	1.00[EUR][1000 genomes]
rs9490256	1.00[EUR][1000 genomes]

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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121509600-121575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:121533000-121566800	Weak transcription	Stomach Mucosa	stomach
3	chr6:121535000-121569200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:121536200-121567200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:121536600-121568200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:121536600-121585400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:121536800-121584400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:121537000-121584600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:121537400-121567800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:121538200-121567000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:121539200-121567600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:121540400-121567800	Weak transcription	Adipose Nuclei	Adipose
13	chr6:121541200-121585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:121544400-121581600	Weak transcription	HSMM	muscle
15	chr6:121544800-121581400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:121552600-121569200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:121552800-121567800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:121554200-121568000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:121554800-121567000	Weak transcription	Placenta	Placenta
20	chr6:121555000-121567200	Weak transcription	Colonic Mucosa	Colon
21	chr6:121555600-121567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:121555600-121568000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:121556600-121581800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:121556800-121567200	Weak transcription	Thymus	Thymus
25	chr6:121556800-121581600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:121557000-121566800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:121557000-121566800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:121557000-121566800	Weak transcription	Lung	lung
29	chr6:121557000-121567600	Weak transcription	HSMMtube	muscle
30	chr6:121557000-121567800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:121557000-121567800	Weak transcription	Pancreas	Pancrea
32	chr6:121557000-121567800	Weak transcription	Right Ventricle	heart
33	chr6:121557000-121568800	Weak transcription	Left Ventricle	heart
34	chr6:121557200-121568000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:121557400-121567800	Weak transcription	Fetal Lung	lung
36	chr6:121560600-121567800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:121562000-121566800	Weak transcription	Aorta	Aorta
38	chr6:121563600-121567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:121565000-121567400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:121565600-121567200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:121565600-121567600	Weak transcription	Brain Anterior Caudate	brain
42	chr6:121565800-121566800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:121565800-121567000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:121566000-121566800	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:121566000-121566800	Strong transcription	Fetal Stomach	stomach
46	chr6:121566000-121566800	Strong transcription	Ovary	ovary
47	chr6:121566000-121567000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:121566000-121567000	Strong transcription	Primary T cells from cord blood	blood
49	chr6:121566000-121567000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:121566000-121567200	Strong transcription	Duodenum Mucosa	Duodenum

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