Variant report

Variant	rs35476990
Chromosome Location	chr9:95911979-95911980
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95902681..95906471-chr9:95910340..95913380,3	MCF-7	breast:
2	chr9:95893058..95897120-chr9:95910165..95913042,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1127857	1.00[ASN][1000 genomes]
rs12004134	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005054	1.00[ASN][1000 genomes]
rs13284407	1.00[ASN][1000 genomes]
rs13284544	1.00[ASN][1000 genomes]
rs13284731	1.00[ASN][1000 genomes]
rs13285019	1.00[ASN][1000 genomes]
rs13285107	1.00[ASN][1000 genomes]
rs13286331	1.00[ASN][1000 genomes]
rs13294417	1.00[ASN][1000 genomes]
rs13297094	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13298119	1.00[ASN][1000 genomes]
rs13299270	1.00[ASN][1000 genomes]
rs13300450	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297115	1.00[ASN][1000 genomes]
rs34476050	1.00[ASN][1000 genomes]
rs36034699	1.00[ASN][1000 genomes]
rs4743906	1.00[ASN][1000 genomes]
rs7035004	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037142	1.00[ASN][1000 genomes]
rs7871317	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35476990	RP11-370F5.4	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95899800-95922200	Weak transcription	Gastric	stomach
2	chr9:95907200-95913200	Weak transcription	HepG2	liver
3	chr9:95907200-95913400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:95907200-95918600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:95907200-95922200	Weak transcription	Pancreas	Pancrea
6	chr9:95907200-95944400	Weak transcription	Right Atrium	heart
7	chr9:95908600-95918600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:95909400-95922000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:95911200-95912000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:95911400-95912000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr9:95911400-95912000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:95911400-95912600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr9:95911600-95912000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr9:95911600-95912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:95911600-95913000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:95911800-95912000	Enhancers	NHLF	lung
17	chr9:95911800-95912800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:95911800-95918400	Weak transcription	GM12878-XiMat	blood

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