Variant report

Variant	rs60076242
Chromosome Location	chr9:96333916-96333917
allele	C/T
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	chr9:96333913-96333918	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96331225..96334018-chr9:96347470..96349122,2	K562	blood:
2	chr9:96212587..96215325-chr9:96332494..96334565,2	MCF-7	breast:

Variant related genes	Relation type
PHF2	TF binding region
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10429558	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11975	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12341488	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554020	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4552973	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59483310	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59582399	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6479482	0.83[EUR][1000 genomes]
rs6479483	0.84[EUR][1000 genomes]
rs6479494	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479495	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7020459	0.84[EUR][1000 genomes]
rs7023933	0.81[AMR][1000 genomes]
rs7025805	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7028729	0.83[EUR][1000 genomes]
rs7036984	0.83[EUR][1000 genomes]
rs7048853	0.80[AMR][1000 genomes]
rs7850322	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7857183	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7860098	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7862998	0.83[EUR][1000 genomes]
rs7870210	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60076242	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs60076242	RP11-165J3.6	cis	Thyroid	GTEx
rs60076242	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96330000-96337200	Weak transcription	NHLF	lung
2	chr9:96330000-96337400	Weak transcription	Hela-S3	cervix
3	chr9:96330000-96337400	Weak transcription	HSMM	muscle
4	chr9:96330200-96335200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:96330200-96335200	Weak transcription	Left Ventricle	heart
6	chr9:96330200-96335600	Weak transcription	Esophagus	oesophagus
7	chr9:96330200-96336400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:96330200-96336400	Weak transcription	Brain Substantia Nigra	brain
9	chr9:96330200-96336600	Weak transcription	Primary T cells from cord blood	blood
10	chr9:96330200-96336600	Weak transcription	Lung	lung
11	chr9:96330200-96336800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:96330200-96336800	Weak transcription	Fetal Lung	lung
13	chr9:96330200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr9:96330200-96337000	Weak transcription	Fetal Intestine Small	intestine
15	chr9:96330200-96337000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:96330200-96337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:96330200-96337200	Weak transcription	Aorta	Aorta
18	chr9:96330200-96337200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:96330200-96337200	Weak transcription	Colonic Mucosa	Colon
20	chr9:96330200-96337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:96330200-96337200	Weak transcription	Osteobl	bone
22	chr9:96330200-96337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:96330200-96337400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:96330200-96337400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:96330200-96337400	Weak transcription	Psoas Muscle	Psoas
26	chr9:96330200-96337400	Weak transcription	NHEK	skin
27	chr9:96330200-96337600	Weak transcription	Right Atrium	heart
28	chr9:96330400-96337000	Weak transcription	Fetal Heart	heart
29	chr9:96330800-96337200	Weak transcription	Pancreas	Pancrea
30	chr9:96331000-96334800	Weak transcription	Fetal Thymus	thymus
31	chr9:96331000-96335800	Weak transcription	Placenta	Placenta
32	chr9:96331000-96336800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:96331000-96336800	Weak transcription	Gastric	stomach
34	chr9:96331000-96336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:96331000-96337000	Weak transcription	Fetal Stomach	stomach
36	chr9:96332000-96336400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:96332200-96336600	Weak transcription	Spleen	Spleen
38	chr9:96332400-96334600	Weak transcription	Thymus	Thymus
39	chr9:96332400-96337400	Weak transcription	Primary B cells from cord blood	blood
40	chr9:96332400-96337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:96332600-96334000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:96332600-96336400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:96332600-96336800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:96332600-96337400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr9:96333200-96336400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:96333400-96336800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:96333400-96337200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:96333400-96337200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:96333600-96336400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:96333600-96337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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