Variant report

Variant	rs9298684
Chromosome Location	chr9:12801148-12801149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12794123..12798425-chr9:12799018..12802796,5	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10122949	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10809846	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10960800	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10960803	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10960804	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10960805	0.85[EUR][1000 genomes]
rs10960808	0.88[EUR][1000 genomes]
rs10960813	0.83[EUR][1000 genomes]
rs12237752	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1318454	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13289069	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34919266	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4397503	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6474732	0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6474733	0.88[EUR][1000 genomes]
rs71474394	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71507332	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7846724	0.88[TSI][hapmap]
rs7859336	0.88[EUR][1000 genomes]
rs957224	0.81[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12785400-12808800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:12785800-12802200	Weak transcription	Left Ventricle	heart
3	chr9:12785800-12813600	Weak transcription	Fetal Intestine Large	intestine
4	chr9:12786000-12813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:12786000-12813600	Weak transcription	Fetal Intestine Small	intestine
6	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:12794800-12811800	Weak transcription	Hela-S3	cervix
8	chr9:12795000-12809400	Weak transcription	HepG2	liver
9	chr9:12795800-12802200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:12795800-12813400	Weak transcription	Fetal Kidney	kidney
11	chr9:12795800-12813800	Weak transcription	Fetal Stomach	stomach
12	chr9:12797200-12809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:12797200-12809800	Weak transcription	Stomach Mucosa	stomach
14	chr9:12797400-12801200	Weak transcription	NHLF	lung
15	chr9:12798600-12801200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:12798600-12803000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:12798600-12805600	Weak transcription	A549	lung
18	chr9:12798600-12809800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:12798600-12812000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:12798600-12812800	Weak transcription	NH-A	brain
21	chr9:12798800-12805600	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:12798800-12808600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:12798800-12811800	Weak transcription	HSMMtube	muscle
24	chr9:12799000-12801200	Weak transcription	NHDF-Ad	bronchial
25	chr9:12799000-12809200	Weak transcription	Osteobl	bone
26	chr9:12799000-12809400	Weak transcription	HMEC	breast
27	chr9:12799200-12802200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:12799200-12805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:12799200-12808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:12799200-12810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:12799400-12808800	Weak transcription	NHEK	skin
32	chr9:12800200-12801200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:12800200-12802200	Enhancers	Fetal Lung	lung

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