Variant report

Variant	rs4946544
Chromosome Location	chr6:121478472-121478473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:121477367..121479870-chr6:121507284..121508935,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10499102	0.90[EUR][1000 genomes]
rs10499103	0.90[EUR][1000 genomes]
rs10499107	1.00[EUR][1000 genomes]
rs10499108	0.90[EUR][1000 genomes]
rs10499110	0.90[EUR][1000 genomes]
rs17052877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17083091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17083156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17083168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17083211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083268	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17083302	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17083356	0.90[EUR][1000 genomes]
rs17083358	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17083360	0.90[EUR][1000 genomes]
rs17083375	0.90[EUR][1000 genomes]
rs17083385	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17083389	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17083397	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17083405	0.90[EUR][1000 genomes]
rs17083417	0.90[EUR][1000 genomes]
rs17083420	0.90[EUR][1000 genomes]
rs17083421	0.90[EUR][1000 genomes]
rs17083432	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2358134	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35710769	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3923664	0.90[EUR][1000 genomes]
rs4144169	1.00[EUR][1000 genomes]
rs4441982	0.90[EUR][1000 genomes]
rs4469335	0.90[EUR][1000 genomes]
rs4487619	1.00[EUR][1000 genomes]
rs4580906	0.90[EUR][1000 genomes]
rs4585597	0.90[EUR][1000 genomes]
rs4945680	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4945683	0.90[EUR][1000 genomes]
rs4946530	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4946534	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4946536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946549	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4946552	0.90[EUR][1000 genomes]
rs4946553	0.90[EUR][1000 genomes]
rs4946554	0.90[EUR][1000 genomes]
rs4946555	0.90[EUR][1000 genomes]
rs4946556	0.90[EUR][1000 genomes]
rs4946557	0.90[EUR][1000 genomes]
rs4946560	0.90[EUR][1000 genomes]
rs4946561	0.90[EUR][1000 genomes]
rs59945135	0.90[EUR][1000 genomes]
rs61550917	0.90[EUR][1000 genomes]
rs6899528	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv604572	chr6:121465011-121544876	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121472600-121481600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:121473400-121480600	Weak transcription	Small Intestine	intestine
3	chr6:121473400-121499000	Weak transcription	Right Ventricle	heart
4	chr6:121474200-121478600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:121474200-121479600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:121474200-121483400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:121474400-121483200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:121474400-121483400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:121474600-121478600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:121474600-121479000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:121474600-121479000	Weak transcription	HSMMtube	muscle
12	chr6:121474600-121481400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:121474600-121485200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:121474600-121508600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:121474800-121479000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:121474800-121484000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:121475000-121479000	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:121475000-121482400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:121475200-121481400	Weak transcription	Brain Germinal Matrix	brain
20	chr6:121475400-121478600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:121475400-121478600	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:121475400-121479000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:121475400-121479400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:121475400-121480400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:121475400-121483000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:121475600-121478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:121475600-121478600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:121475600-121478600	Weak transcription	Left Ventricle	heart
29	chr6:121475600-121478600	Weak transcription	Ovary	ovary
30	chr6:121475600-121479600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:121475600-121479600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:121475600-121479600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:121475600-121480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:121475600-121480400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:121475600-121480600	Weak transcription	Aorta	Aorta
36	chr6:121475600-121481000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:121475600-121481400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:121475600-121481400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:121475600-121481800	Weak transcription	Pancreas	Pancrea
40	chr6:121475600-121482400	Weak transcription	Placenta	Placenta
41	chr6:121475600-121483600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:121475600-121508600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:121475800-121483600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:121476000-121478600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:121476000-121479000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:121477000-121482200	Weak transcription	Fetal Heart	heart
47	chr6:121477400-121478600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:121477400-121482000	Weak transcription	Fetal Kidney	kidney
49	chr6:121477400-121485000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:121477600-121479800	Weak transcription	Psoas Muscle	Psoas

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