Variant report

Variant	rs9355442
Chromosome Location	chr6:164259420-164259421
allele	A/G
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	KAP1	chr6:164258291-164259545	U2OS	brain:	n/a	n/a
2	SETDB1	chr6:164258740-164259428	U2OS	brain:	n/a	n/a
3	KAP1	chr6:164258279-164259493	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:164242074..164244714-chr6:164257736..164260576,2	K562	blood:

Variant related genes	Relation type
RN7SL366P	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1028485	0.83[EUR][1000 genomes]
rs1040641	0.88[ASN][1000 genomes]
rs10806784	0.83[EUR][1000 genomes]
rs1111705	0.88[ASN][1000 genomes]
rs13203619	0.96[ASN][1000 genomes]
rs1555229	0.81[CHB][hapmap]
rs2015261	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2321978	0.80[CHB][hapmap]
rs4709760	0.88[ASN][1000 genomes]
rs4709765	0.88[ASN][1000 genomes]
rs4709766	0.88[ASN][1000 genomes]
rs4709773	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4709775	0.83[EUR][1000 genomes]
rs6925383	0.81[ASN][1000 genomes]
rs7762180	0.81[ASN][1000 genomes]
rs7765258	0.83[ASN][1000 genomes]
rs8180622	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs880095	0.90[ASN][1000 genomes]
rs9295231	0.87[ASN][1000 genomes]
rs9295232	0.90[ASN][1000 genomes]
rs9295233	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9346974	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9346975	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9347790	0.82[ASN][1000 genomes]
rs9347791	0.87[ASN][1000 genomes]
rs9347792	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9347793	0.88[ASN][1000 genomes]
rs9347798	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9347799	0.84[EUR][1000 genomes]
rs9355439	0.88[ASN][1000 genomes]
rs9355440	0.90[ASN][1000 genomes]
rs9356152	0.83[ASN][1000 genomes]
rs9356153	0.83[ASN][1000 genomes]
rs9356156	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356159	0.82[EUR][1000 genomes]
rs9356160	0.83[EUR][1000 genomes]
rs9364703	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9365619	0.90[ASN][1000 genomes]
rs9365620	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9365624	0.83[EUR][1000 genomes]
rs9365625	0.83[EUR][1000 genomes]
rs9456885	0.88[ASN][1000 genomes]
rs9458911	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1798922	chr6:164257563-164298780	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9355442	NCRNA00241	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164256800-164260600	Enhancers	Fetal Heart	heart
2	chr6:164257800-164259600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:164258400-164259600	Active TSS	Ovary	ovary
4	chr6:164259000-164260200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:164259000-164260200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:164259200-164259600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:164259200-164259800	Enhancers	Fetal Lung	lung
8	chr6:164259200-164260000	Enhancers	Fetal Stomach	stomach
9	chr6:164259200-164260200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:164259200-164261200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:164259200-164261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:164259200-164262400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:164259200-164262600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:164259400-164259600	Enhancers	Brain Substantia Nigra	brain
15	chr6:164259400-164259800	Enhancers	Fetal Brain Female	brain
16	chr6:164259400-164260400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:164259400-164260600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:164259400-164260600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:164259400-164260800	Enhancers	Brain Germinal Matrix	brain
20	chr6:164259400-164261200	Weak transcription	Fetal Kidney	kidney
21	chr6:164259400-164262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:164259400-164264200	Weak transcription	Fetal Brain Male	brain

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