Variant report

Variant	rs11961542
Chromosome Location	chr6:128560501-128560502
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	chr6:128551695..128554319-chr6:128560402..128562022,2	MCF-7	breast:
2	chr6:128552552..128554388-chr6:128558888..128560797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10485160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055654	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055776	0.84[ASN][1000 genomes]
rs1543376	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17055441	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17055472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073161	0.84[ASN][1000 genomes]
rs2076572	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813371	0.84[ASN][1000 genomes]
rs3813372	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813373	0.84[ASN][1000 genomes]
rs4140541	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140542	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4243494	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421217	0.86[ASN][1000 genomes]
rs4483000	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4897252	0.83[ASN][1000 genomes]
rs61422755	0.85[ASN][1000 genomes]
rs61583694	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928143	0.91[ASN][1000 genomes]
rs6933029	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6938118	0.86[ASN][1000 genomes]
rs730202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73590673	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753945	0.86[ASN][1000 genomes]
rs7755473	0.84[ASN][1000 genomes]
rs7755836	0.95[ASN][1000 genomes]
rs7773849	0.95[ASN][1000 genomes]
rs9321113	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9372886	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372887	0.82[ASN][1000 genomes]
rs9375551	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375552	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375554	0.84[ASN][1000 genomes]
rs9375555	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375556	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375557	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375558	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9385452	0.84[ASN][1000 genomes]
rs9385454	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9385455	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388618	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9388619	0.86[ASN][1000 genomes]
rs9388621	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388622	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9388624	0.84[ASN][1000 genomes]
rs9388625	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388626	0.95[ASN][1000 genomes]
rs9388627	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398866	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9398867	0.82[ASN][1000 genomes]
rs9398868	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402023	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9402024	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9402025	0.84[ASN][1000 genomes]
rs9402027	0.84[ASN][1000 genomes]
rs9402028	0.84[ASN][1000 genomes]
rs9402029	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402030	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402031	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9402032	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9784773	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9784880	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
7	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
8	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
10	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
11	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:128532000-128561000	Weak transcription	Osteobl	bone
14	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
15	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:128540200-128561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:128540600-128561000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:128544200-128562400	Weak transcription	Gastric	stomach
23	chr6:128544200-128563200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:128551400-128561000	Weak transcription	Right Atrium	heart
25	chr6:128551400-128565800	Weak transcription	Psoas Muscle	Psoas
26	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
27	chr6:128552600-128562400	Weak transcription	Fetal Intestine Small	intestine
28	chr6:128553200-128573800	Weak transcription	NHLF	lung
29	chr6:128553400-128564400	Weak transcription	Lung	lung
30	chr6:128553800-128561000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:128553800-128570600	Weak transcription	Liver	Liver
32	chr6:128554000-128561000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:128554600-128564200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:128555000-128561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:128555000-128564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:128555200-128561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:128555200-128561000	Weak transcription	Right Ventricle	heart
38	chr6:128555200-128584400	Weak transcription	HMEC	breast
39	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:128555800-128564800	Weak transcription	Fetal Brain Female	brain
41	chr6:128556600-128564400	Strong transcription	HepG2	liver
42	chr6:128557000-128561000	Weak transcription	Fetal Kidney	kidney
43	chr6:128557000-128561000	Weak transcription	NHDF-Ad	bronchial
44	chr6:128557000-128561000	Weak transcription	NHEK	skin
45	chr6:128557800-128561000	Weak transcription	Thymus	Thymus
46	chr6:128558400-128561200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:128558400-128561400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:128558400-128561400	Enhancers	Brain Substantia Nigra	brain
49	chr6:128558400-128561600	Enhancers	Brain Angular Gyrus	brain
50	chr6:128558400-128561800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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