Variant report

Variant	rs1743942
Chromosome Location	chr6:134557779-134557780
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	chr6:134553108..134554693-chr6:134556354..134559341,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1631657	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631879	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17063535	0.98[ASN][1000 genomes]
rs17063545	1.00[ASN][1000 genomes]
rs17063554	1.00[ASN][1000 genomes]
rs17063563	0.86[ASN][1000 genomes]
rs1743937	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1743938	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743939	0.87[AFR][1000 genomes]
rs1743940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743941	0.84[AFR][1000 genomes]
rs1743945	0.83[AFR][1000 genomes]
rs1743946	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1763509	0.88[ASN][1000 genomes]
rs4896029	0.84[ASN][1000 genomes]
rs57109798	0.95[ASN][1000 genomes]
rs62425170	1.00[ASN][1000 genomes]
rs62425189	1.00[ASN][1000 genomes]
rs62425190	1.00[ASN][1000 genomes]
rs744196	0.85[ASN][1000 genomes]
rs9385680	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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:58 , 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	chr6:134551400-134558800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:134551400-134559600	Weak transcription	Adipose Nuclei	Adipose
4	chr6:134551400-134560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:134551600-134561600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:134552200-134558600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr6:134553800-134558200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr6:134554800-134559200	Weak transcription	Brain Angular Gyrus	brain
9	chr6:134554800-134559200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:134556200-134558000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:134556200-134558000	Enhancers	K562	blood
12	chr6:134556200-134558000	Enhancers	Osteobl	bone
13	chr6:134556200-134558200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:134556200-134558600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:134556200-134558800	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:134556200-134559000	Enhancers	Primary B cells from cord blood	blood
17	chr6:134556400-134560200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:134556800-134557800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:134556800-134557800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:134556800-134557800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:134556800-134557800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:134556800-134558000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:134556800-134558000	Enhancers	HUVEC	blood vessel
24	chr6:134556800-134558000	Enhancers	NHDF-Ad	bronchial
25	chr6:134556800-134558200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:134556800-134558400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:134556800-134558400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr6:134556800-134558800	Enhancers	Pancreas	Pancrea
29	chr6:134557000-134557800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:134557000-134557800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:134557000-134557800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:134557000-134557800	Enhancers	HMEC	breast
33	chr6:134557000-134557800	Enhancers	NH-A	brain
34	chr6:134557000-134558000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:134557000-134558000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:134557000-134558000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:134557000-134558000	Enhancers	Hela-S3	cervix
38	chr6:134557000-134558200	Enhancers	NHLF	lung
39	chr6:134557200-134557800	Flanking Active TSS	GM12878-XiMat	blood
40	chr6:134557200-134558200	Enhancers	Brain Cingulate Gyrus	brain
41	chr6:134557200-134558600	Enhancers	Brain Anterior Caudate	brain
42	chr6:134557200-134559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:134557200-134560200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:134557200-134560200	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:134557200-134561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:134557400-134557800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:134557400-134558000	Enhancers	Primary T cells from cord blood	blood
48	chr6:134557400-134558000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr6:134557400-134558600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr6:134557400-134560200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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