Variant report

Variant	rs6560508
Chromosome Location	chr9:78830150-78830151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:78826468..78829058-chr9:78829509..78831347,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10746996	0.97[ASN][1000 genomes]
rs10746997	0.88[ASN][1000 genomes]
rs10781345	0.82[ASN][1000 genomes]
rs10781346	0.87[ASN][1000 genomes]
rs10781348	0.88[ASN][1000 genomes]
rs10869733	0.80[ASN][1000 genomes]
rs10869736	0.88[ASN][1000 genomes]
rs10869737	0.88[ASN][1000 genomes]
rs11144801	0.88[ASN][1000 genomes]
rs11144804	0.87[ASN][1000 genomes]
rs12336492	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495255	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3913046	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4545165	0.88[ASN][1000 genomes]
rs4745528	0.88[ASN][1000 genomes]
rs7033364	0.87[ASN][1000 genomes]
rs7854188	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs952503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs990559	0.87[ASN][1000 genomes]
rs990560	0.88[ASN][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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv893476	chr9:78768830-78887992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78814000-78848200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:78824200-78832800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:78827400-78832000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:78827800-78832600	Enhancers	NHDF-Ad	bronchial
5	chr9:78828400-78831800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:78828400-78831800	Enhancers	HMEC	breast
7	chr9:78828400-78831800	Enhancers	HSMM	muscle
8	chr9:78828600-78831400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:78828600-78831800	Enhancers	NHEK	skin
10	chr9:78828600-78834200	Enhancers	NH-A	brain
11	chr9:78828800-78833800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:78828800-78834600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:78829000-78831800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:78829200-78832000	Weak transcription	Fetal Intestine Large	intestine
15	chr9:78829200-78832200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:78829400-78831200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:78829400-78831600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:78829400-78831800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:78829400-78832200	Enhancers	NHLF	lung
20	chr9:78829600-78831800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:78829600-78831800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:78829600-78831800	Enhancers	Osteobl	bone
23	chr9:78829800-78830200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr9:78829800-78831400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr9:78829800-78831400	Enhancers	A549	lung
26	chr9:78829800-78831800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:78829800-78831800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:78829800-78832200	Enhancers	HUVEC	blood vessel
29	chr9:78829800-78834200	Enhancers	HSMMtube	muscle
30	chr9:78830000-78830200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr9:78830000-78830400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr9:78830000-78830600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:78830000-78830600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:78830000-78830800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:78830000-78831200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:78830000-78831400	Strong transcription	Fetal Intestine Small	intestine

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