Variant report

Variant	rs4140542
Chromosome Location	chr6:128567337-128567338
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	chr6:128566524..128568346-chr6:128578844..128580806,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10485160	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11961542	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12055654	0.82[ASN][1000 genomes]
rs12055776	0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17055472	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17055477	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2073161	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076572	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4140541	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4483000	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61422755	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61583694	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6930547	0.88[ASN][1000 genomes]
rs730202	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73590673	0.82[ASN][1000 genomes]
rs742736	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7755473	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9321113	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9372886	0.82[ASN][1000 genomes]
rs9372887	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375553	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9375554	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375555	0.82[ASN][1000 genomes]
rs9375556	0.82[ASN][1000 genomes]
rs9375557	0.82[ASN][1000 genomes]
rs9375558	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9385452	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9385455	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9388623	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9388624	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388625	0.82[ASN][1000 genomes]
rs9388627	0.82[ASN][1000 genomes]
rs9398864	0.88[ASN][1000 genomes]
rs9398865	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398867	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398868	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9402025	0.84[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9402027	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402028	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402029	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9402030	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9402031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402032	0.80[ASN][1000 genomes]
rs9784773	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9784880	0.80[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	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128492600-128567800	Weak transcription	Ovary	ovary
2	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
8	chr6:128553200-128573800	Weak transcription	NHLF	lung
9	chr6:128553800-128570600	Weak transcription	Liver	Liver
10	chr6:128555200-128584400	Weak transcription	HMEC	breast
11	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:128559600-128570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:128561400-128567800	Weak transcription	Right Ventricle	heart
14	chr6:128561400-128573000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:128561400-128587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:128561600-128567600	Weak transcription	Brain Angular Gyrus	brain
17	chr6:128561600-128569200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:128561600-128573800	Weak transcription	Thymus	Thymus
19	chr6:128562400-128576600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:128562600-128567400	Weak transcription	Brain Anterior Caudate	brain
21	chr6:128562600-128573600	Weak transcription	Primary T cells from cord blood	blood
22	chr6:128562800-128567600	Weak transcription	Brain Substantia Nigra	brain
23	chr6:128562800-128567600	Weak transcription	Fetal Intestine Large	intestine
24	chr6:128562800-128567800	Weak transcription	Right Atrium	heart
25	chr6:128562800-128568000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:128562800-128573000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:128562800-128573000	Weak transcription	Aorta	Aorta
28	chr6:128562800-128573800	Weak transcription	Gastric	stomach
29	chr6:128562800-128579800	Weak transcription	Left Ventricle	heart
30	chr6:128562800-128588200	Weak transcription	HUVEC	blood vessel
31	chr6:128563000-128570600	Weak transcription	HSMMtube	muscle
32	chr6:128563000-128573000	Weak transcription	NH-A	brain
33	chr6:128563000-128574000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:128563000-128585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:128563200-128567600	Weak transcription	Fetal Intestine Small	intestine
36	chr6:128563800-128567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:128564400-128583400	Weak transcription	HepG2	liver
38	chr6:128564400-128588600	Weak transcription	NHEK	skin
39	chr6:128564600-128573800	Weak transcription	Fetal Thymus	thymus
40	chr6:128565000-128573000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:128565800-128570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:128566000-128572600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:128566400-128579800	Weak transcription	Psoas Muscle	Psoas
44	chr6:128566800-128567800	Weak transcription	Fetal Heart	heart
45	chr6:128566800-128570000	Weak transcription	HSMM	muscle
46	chr6:128566800-128573000	Weak transcription	Osteobl	bone
47	chr6:128567000-128567400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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