Variant report

Variant	rs10960804
Chromosome Location	chr9:12808688-12808689
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	chr9:12777697..12781582-chr9:12805623..12809956,4	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10122949	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10809846	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10960800	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10960803	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10960805	0.85[EUR][1000 genomes]
rs10960808	0.88[EUR][1000 genomes]
rs10960813	0.83[EUR][1000 genomes]
rs1318454	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13289069	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34919266	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4397503	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6474732	0.88[EUR][1000 genomes]
rs6474733	0.88[EUR][1000 genomes]
rs71474394	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71507332	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7859336	0.88[EUR][1000 genomes]
rs9298684	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs957224	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 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	chr9:12798600-12809800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:12798600-12812000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:12798600-12812800	Weak transcription	NH-A	brain
15	chr9:12798800-12811800	Weak transcription	HSMMtube	muscle
16	chr9:12799000-12809200	Weak transcription	Osteobl	bone
17	chr9:12799000-12809400	Weak transcription	HMEC	breast
18	chr9:12799200-12808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:12799200-12810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:12799400-12808800	Weak transcription	NHEK	skin
21	chr9:12802400-12812800	Weak transcription	HUVEC	blood vessel
22	chr9:12802400-12814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:12802600-12808800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:12802800-12809000	Weak transcription	NHDF-Ad	bronchial
25	chr9:12803000-12811400	Weak transcription	NHLF	lung
26	chr9:12803400-12811400	Weak transcription	Fetal Lung	lung
27	chr9:12803800-12811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:12805400-12809000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:12806000-12811400	Weak transcription	A549	lung
30	chr9:12806200-12809000	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:12806200-12809400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:12808600-12809000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:12808600-12810200	Weak transcription	Aorta	Aorta
34	chr9:12808600-12810400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain

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