Variant report

Variant	rs56998622
Chromosome Location	chr9:104250399-104250400
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:104250356-104250413	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104159029..104163428-chr9:104247830..104250587,4	K562	blood:

Variant related genes	Relation type
TMEM246	TF binding region
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11793946	0.81[ASN][1000 genomes]
rs16920437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920477	0.81[ASN][1000 genomes]
rs1929483	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411396	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813523	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575836	0.81[ASN][1000 genomes]
rs62575837	0.81[ASN][1000 genomes]
rs72745305	0.81[ASN][1000 genomes]
rs7872953	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised 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	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104249800-104250400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr9:104249800-104250800	Enhancers	Fetal Heart	heart
3	chr9:104250000-104250400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr9:104250000-104250400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr9:104250000-104250400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:104250000-104250400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:104250000-104250400	Weak transcription	Brain Angular Gyrus	brain
8	chr9:104250000-104250400	Enhancers	Brain Hippocampus Middle	brain
9	chr9:104250000-104250400	Enhancers	Colon Smooth Muscle	Colon
10	chr9:104250000-104250400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr9:104250000-104250400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr9:104250000-104250600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:104250000-104250600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:104250000-104250600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr9:104250000-104250600	Enhancers	Fetal Intestine Small	intestine
16	chr9:104250000-104250600	Enhancers	Stomach Mucosa	stomach
17	chr9:104250000-104250800	Enhancers	Fetal Intestine Large	intestine
18	chr9:104250000-104250800	Enhancers	NHEK	skin
19	chr9:104250000-104253600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:104250200-104250600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:104250200-104250800	Enhancers	Pancreatic Islets	Pancreatic Islet

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