Variant report

Variant	rs12346586
Chromosome Location	chr9:96334915-96334916
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	POLR2A	chr9:96334558-96335196	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:96334704-96334987	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:96334886-96335943	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96207153..96210037-chr9:96334442..96336797,2	MCF-7	breast:
2	chr9:96333987..96335844-chr9:111755686..111758072,2	MCF-7	breast:
3	chr9:96334438..96336370-chr9:96418829..96421734,2	MCF-7	breast:
4	chr9:96300899..96303747-chr9:96334511..96337154,2	MCF-7	breast:

Variant related genes	Relation type
PHF2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10116959	1.00[EUR][1000 genomes]
rs10117404	1.00[EUR][1000 genomes]
rs10118281	1.00[EUR][1000 genomes]
rs10118574	1.00[EUR][1000 genomes]
rs10118955	1.00[EUR][1000 genomes]
rs10121548	1.00[EUR][1000 genomes]
rs10121798	1.00[EUR][1000 genomes]
rs10123186	1.00[EUR][1000 genomes]
rs10123412	1.00[EUR][1000 genomes]
rs10992758	1.00[EUR][1000 genomes]
rs10992822	1.00[EUR][1000 genomes]
rs1123475	1.00[EUR][1000 genomes]
rs12337821	1.00[EUR][1000 genomes]
rs12340447	1.00[EUR][1000 genomes]
rs12344186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12348843	1.00[EUR][1000 genomes]
rs12349453	1.00[EUR][1000 genomes]
rs12350884	1.00[EUR][1000 genomes]
rs16909307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28406634	1.00[EUR][1000 genomes]
rs28464341	1.00[EUR][1000 genomes]
rs28523540	1.00[EUR][1000 genomes]
rs28630935	1.00[EUR][1000 genomes]
rs28666855	1.00[EUR][1000 genomes]
rs28728320	1.00[EUR][1000 genomes]
rs28848910	1.00[EUR][1000 genomes]
rs58925215	1.00[EUR][1000 genomes]
rs61301026	1.00[EUR][1000 genomes]
rs61467488	1.00[EUR][1000 genomes]
rs61636268	1.00[EUR][1000 genomes]
rs7021423	1.00[EUR][1000 genomes]
rs7022246	1.00[EUR][1000 genomes]
rs7033089	1.00[EUR][1000 genomes]
rs73651245	1.00[EUR][1000 genomes]
rs73651251	1.00[EUR][1000 genomes]
rs73651269	1.00[EUR][1000 genomes]
rs73651270	1.00[EUR][1000 genomes]
rs73651297	1.00[EUR][1000 genomes]
rs73651298	1.00[EUR][1000 genomes]
rs7848429	1.00[EUR][1000 genomes]
rs7850596	1.00[EUR][1000 genomes]
rs7854758	1.00[EUR][1000 genomes]
rs7856259	1.00[EUR][1000 genomes]
rs7870048	1.00[EUR][1000 genomes]
rs7871486	1.00[EUR][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

No data

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	chr9:96331000-96335800	Weak transcription	Placenta	Placenta
31	chr9:96331000-96336800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr9:96331000-96336800	Weak transcription	Gastric	stomach
33	chr9:96331000-96336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:96331000-96337000	Weak transcription	Fetal Stomach	stomach
35	chr9:96332000-96336400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:96332200-96336600	Weak transcription	Spleen	Spleen
37	chr9:96332400-96337400	Weak transcription	Primary B cells from cord blood	blood
38	chr9:96332400-96337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:96332600-96336400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr9:96332600-96336800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:96332600-96337400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr9:96333200-96336400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:96333400-96336800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:96333400-96337200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:96333400-96337200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:96333600-96336400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:96333600-96337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:96333800-96337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:96333800-96337200	Weak transcription	Fetal Brain Female	brain
50	chr9:96333800-96337400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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