Variant report

Variant	rs742556
Chromosome Location	chr6:1633682-1633683
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	chr6:1609773..1613504-chr6:1633315..1635926,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2569842	0.84[ASW][hapmap];0.82[CEU][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs2569846	0.84[ASW][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs2569855	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2745611	0.95[CEU][hapmap]
rs2745612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs742557	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378643	0.92[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs742556	MYO6	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1625200-1634000	Weak transcription	Gastric	stomach
2	chr6:1625800-1639400	Weak transcription	Ovary	ovary
3	chr6:1626200-1636800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:1626400-1637000	Weak transcription	Pancreas	Pancrea
5	chr6:1629000-1634400	Weak transcription	Aorta	Aorta
6	chr6:1629800-1636400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:1630000-1633800	Weak transcription	Lung	lung
8	chr6:1630200-1635400	Weak transcription	Right Atrium	heart
9	chr6:1630800-1633800	Weak transcription	Fetal Intestine Small	intestine
10	chr6:1630800-1635800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:1631000-1634200	Weak transcription	HepG2	liver
12	chr6:1631200-1636800	Weak transcription	Esophagus	oesophagus
13	chr6:1631400-1634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:1631400-1635000	Weak transcription	Fetal Thymus	thymus
15	chr6:1631400-1635200	Weak transcription	HUVEC	blood vessel
16	chr6:1631600-1646000	Weak transcription	Osteobl	bone
17	chr6:1632200-1635000	Weak transcription	Placenta	Placenta
18	chr6:1632600-1639800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:1633000-1679800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:1633400-1637600	Weak transcription	Stomach Mucosa	stomach

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