Variant report

Variant	rs10960800
Chromosome Location	chr9:12802214-12802215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12786137..12788108-chr9:12801967..12804015,2	MCF-7	breast:
2	chr9:12774319..12775976-chr9:12801872..12803906,2	MCF-7	breast:
3	chr9:12794123..12798425-chr9:12799018..12802796,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10122949	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10809846	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10960803	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10960804	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10960805	0.89[EUR][1000 genomes]
rs10960808	0.84[EUR][1000 genomes]
rs10960813	0.86[EUR][1000 genomes]
rs1318454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289069	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34919266	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4397503	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6474732	0.84[EUR][1000 genomes]
rs6474733	0.84[EUR][1000 genomes]
rs71474394	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71507332	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859336	0.84[EUR][1000 genomes]
rs9298684	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs957224	0.86[AMR][1000 genomes];1.00[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:34 , 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	chr9:12785800-12813600	Weak transcription	Fetal Intestine Large	intestine
3	chr9:12786000-12813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:12786000-12813600	Weak transcription	Fetal Intestine Small	intestine
5	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:12794800-12811800	Weak transcription	Hela-S3	cervix
7	chr9:12795000-12809400	Weak transcription	HepG2	liver
8	chr9:12795800-12813400	Weak transcription	Fetal Kidney	kidney
9	chr9:12795800-12813800	Weak transcription	Fetal Stomach	stomach
10	chr9:12797200-12809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:12797200-12809800	Weak transcription	Stomach Mucosa	stomach
12	chr9:12798600-12803000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:12798600-12805600	Weak transcription	A549	lung
14	chr9:12798600-12809800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:12798600-12812000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:12798600-12812800	Weak transcription	NH-A	brain
17	chr9:12798800-12805600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:12798800-12808600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:12798800-12811800	Weak transcription	HSMMtube	muscle
20	chr9:12799000-12809200	Weak transcription	Osteobl	bone
21	chr9:12799000-12809400	Weak transcription	HMEC	breast
22	chr9:12799200-12805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:12799200-12808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:12799200-12810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:12799400-12808800	Weak transcription	NHEK	skin
26	chr9:12801200-12802800	Enhancers	NHDF-Ad	bronchial
27	chr9:12801400-12802400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:12801400-12802400	Enhancers	HUVEC	blood vessel
29	chr9:12801800-12802400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:12802200-12802600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:12802200-12802600	Enhancers	Left Ventricle	heart
32	chr9:12802200-12802600	Weak transcription	NHLF	lung
33	chr9:12802200-12803400	Genic enhancers	Fetal Lung	lung
34	chr9:12802200-12804400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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