Variant report

Variant	rs11668588
Chromosome Location	chr19:39264973-39264974
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	chr19:39264503..39266421-chr19:39288858..39290428,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10853720	1.00[ASN][1000 genomes]
rs11083479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670270	0.98[ASN][1000 genomes]
rs11671165	0.94[ASN][1000 genomes]
rs12151271	0.88[ASN][1000 genomes]
rs12609991	1.00[ASN][1000 genomes]
rs12611054	1.00[ASN][1000 genomes]
rs12611426	1.00[ASN][1000 genomes]
rs59724109	0.98[ASN][1000 genomes]
rs60767833	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063592	chr19:39257977-39287265	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39246400-39270800	Weak transcription	K562	blood
2	chr19:39254200-39265400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39261000-39265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:39261000-39269400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39262200-39274800	Weak transcription	Fetal Intestine Large	intestine
6	chr19:39264200-39265000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr19:39264200-39266200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39264200-39266400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr19:39264200-39266400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:39264200-39266600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:39264200-39266600	Enhancers	HMEC	breast
12	chr19:39264200-39266600	Enhancers	NHEK	skin
13	chr19:39264400-39265000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr19:39264400-39265000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39264400-39265000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:39264400-39265000	Enhancers	HepG2	liver
17	chr19:39264600-39265200	Enhancers	Fetal Muscle Trunk	muscle
18	chr19:39264600-39265600	Enhancers	Spleen	Spleen
19	chr19:39264600-39265800	Enhancers	Stomach Mucosa	stomach
20	chr19:39264600-39266200	Enhancers	Esophagus	oesophagus
21	chr19:39264800-39266000	Weak transcription	A549	lung
22	chr19:39264800-39274800	Weak transcription	Fetal Intestine Small	intestine

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