Variant report

Variant	rs1743939
Chromosome Location	chr6:134560518-134560519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1631024	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1631657	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1631879	0.87[AFR][1000 genomes]
rs1743937	0.86[AFR][1000 genomes]
rs1743938	1.00[ASW][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1743940	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1743941	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1743942	0.87[AFR][1000 genomes]
rs1743945	0.93[CEU][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1743946	0.81[YRI][hapmap]
rs6569935	0.85[EUR][1000 genomes]
rs7759115	0.84[AFR][1000 genomes]
rs9385680	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492292	chr6:134464255-135028540	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1026369	chr6:134468470-135122264	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv538444	chr6:134468470-135122264	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	nsv1018677	chr6:134512542-134638259	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv538445	chr6:134512542-134638259	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1023931	chr6:134512542-134668702	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv538446	chr6:134512542-134668702	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134551000-134564000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:134551600-134561600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:134557200-134561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:134557400-134561800	Enhancers	Brain Hippocampus Middle	brain
5	chr6:134557600-134561600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:134557800-134561000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:134557800-134561600	Weak transcription	HMEC	breast
8	chr6:134557800-134562000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:134557800-134571000	Weak transcription	NH-A	brain
10	chr6:134558000-134561000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:134558000-134561400	Weak transcription	NHEK	skin
12	chr6:134558000-134561600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:134558000-134561600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:134558200-134561600	Weak transcription	GM12878-XiMat	blood
15	chr6:134559000-134561400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:134559200-134560800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:134559200-134561000	Enhancers	Brain Germinal Matrix	brain
18	chr6:134559200-134561200	Enhancers	Brain Angular Gyrus	brain
19	chr6:134559200-134561200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr6:134559200-134561200	Enhancers	Brain Substantia Nigra	brain
21	chr6:134559200-134561200	Enhancers	HepG2	liver
22	chr6:134559200-134562400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:134559200-134563200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:134559400-134561000	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:134559400-134562800	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:134559600-134560600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:134559600-134562000	Enhancers	Adipose Nuclei	Adipose
28	chr6:134560000-134560600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:134560000-134562800	Enhancers	Primary B cells from cord blood	blood
30	chr6:134560000-134562800	Enhancers	Primary T cells from cord blood	blood
31	chr6:134560000-134563200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:134560000-134563200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:134560200-134560600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:134560200-134560600	Enhancers	Esophagus	oesophagus
35	chr6:134560200-134561000	Enhancers	Ovary	ovary
36	chr6:134560200-134561000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:134560200-134561200	Enhancers	Pancreas	Pancrea
38	chr6:134560200-134561200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:134560200-134561200	Enhancers	Spleen	Spleen
40	chr6:134560200-134561200	Enhancers	K562	blood
41	chr6:134560200-134562000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr6:134560200-134562200	Enhancers	Fetal Muscle Leg	muscle
43	chr6:134560200-134562600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr6:134560200-134562800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:134560200-134562800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:134560200-134563400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:134560200-134563400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr6:134560200-134563400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:134560200-134563400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:134560200-134563400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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