Variant report

Variant	rs12555417
Chromosome Location	chr9:110041042-110041043
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	STAT3	chr9:110040790-110041775	MCF10A-Er-Src	breast:	n/a	chr9:110041570-110041581

No.	Distal block	Cell Line	Cell type
1	chr9:110022283..110024488-chr9:110040936..110043082,2	MCF-7	breast:
2	chr9:110014211..110018622-chr9:110040932..110043716,4	MCF-7	breast:
3	chr9:110034708..110043058-chr9:110043083..110050663,16	MCF-7	breast:
4	chr9:110037400..110041134-chr9:110041455..110046032,7	K562	blood:

Variant related genes	Relation type
RAD23B	TF binding region
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10113916	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119641	0.99[ASN][1000 genomes]
rs10122970	1.00[ASN][1000 genomes]
rs10481632	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739236	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816474	0.90[AMR][1000 genomes]
rs10816477	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816485	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816490	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816491	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978767	0.90[AMR][1000 genomes]
rs10978775	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978776	1.00[ASN][1000 genomes]
rs10978777	1.00[ASN][1000 genomes]
rs10978791	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12342066	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345455	1.00[ASN][1000 genomes]
rs1519050	0.82[AMR][1000 genomes]
rs1805329	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2005143	0.95[ASN][1000 genomes]
rs2417776	1.00[ASN][1000 genomes]
rs2417784	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2808362	0.82[AMR][1000 genomes]
rs2808363	0.82[AMR][1000 genomes]
rs2808365	0.82[AMR][1000 genomes]
rs28534368	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28769087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28848858	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61701375	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698475	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7036284	1.00[ASN][1000 genomes]
rs7040217	0.92[ASN][1000 genomes]
rs7041137	0.92[ASN][1000 genomes]
rs7861304	0.83[AMR][1000 genomes]
rs7867544	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7873745	0.99[ASN][1000 genomes]
rs817836	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817838	0.87[ASN][1000 genomes]
rs817839	0.87[ASN][1000 genomes]
rs817840	0.87[ASN][1000 genomes]
rs817841	0.87[ASN][1000 genomes]
rs817843	0.87[ASN][1000 genomes]
rs817844	0.87[ASN][1000 genomes]
rs817845	0.87[ASN][1000 genomes]
rs817847	0.81[ASN][1000 genomes]
rs942291	1.00[ASN][1000 genomes]
rs9632893	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9969728	1.00[ASN][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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110035600-110044600	Enhancers	Placenta	Placenta
2	chr9:110036400-110044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:110037800-110044000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:110038000-110042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:110038000-110042200	Weak transcription	NHEK	skin
6	chr9:110038000-110043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:110038000-110044400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:110038000-110044400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:110038000-110044400	Weak transcription	NH-A	brain
10	chr9:110038200-110042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:110038200-110042200	Weak transcription	HMEC	breast
12	chr9:110038400-110043200	Weak transcription	GM12878-XiMat	blood
13	chr9:110039000-110042800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:110039000-110043000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:110039400-110042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:110039600-110043400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:110039600-110044400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:110039800-110043200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:110039800-110044400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:110039800-110044400	Weak transcription	Adipose Nuclei	Adipose
21	chr9:110039800-110044400	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:110039800-110044400	Weak transcription	A549	lung
23	chr9:110040000-110042800	Weak transcription	NHDF-Ad	bronchial
24	chr9:110040000-110042800	Weak transcription	Osteobl	bone
25	chr9:110040000-110044000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:110040200-110043000	Weak transcription	NHLF	lung
27	chr9:110040200-110044200	Weak transcription	HSMMtube	muscle
28	chr9:110040400-110043200	Weak transcription	Psoas Muscle	Psoas
29	chr9:110040400-110044000	Weak transcription	HSMM	muscle
30	chr9:110040400-110044200	Weak transcription	Fetal Heart	heart
31	chr9:110040400-110044200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:110040400-110044400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:110040400-110044400	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:110040400-110044600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:110040400-110044600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:110040400-110044600	Weak transcription	Fetal Stomach	stomach
37	chr9:110040600-110043400	Enhancers	Primary neutrophils fromperipheralblood	blood

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