Variant report

Variant	rs9471538
Chromosome Location	chr6:12347582-12347583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12341393..12343735-chr6:12346097..12348684,2	MCF-7	breast:
2	chr6:12341804..12346306-chr6:12347487..12351106,5	MCF-7	breast:
3	chr6:12334406..12337144-chr6:12347529..12350449,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10807258	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2095344	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2095345	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184329	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2327544	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462681	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9462684	0.85[AMR][1000 genomes];0.91[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	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv528681	chr6:12340034-12362219	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9471538	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12337200-12348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:12340800-12348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:12341000-12348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:12343200-12348800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:12343200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:12343200-12351400	Weak transcription	Colonic Mucosa	Colon
7	chr6:12344200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:12344400-12348600	Weak transcription	NHEK	skin
9	chr6:12344400-12348800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:12344400-12348800	Weak transcription	NH-A	brain
11	chr6:12344600-12348600	Weak transcription	Hela-S3	cervix
12	chr6:12344600-12348800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:12344600-12349200	Enhancers	A549	lung
14	chr6:12344600-12349800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:12344800-12348600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:12344800-12348600	Weak transcription	HUVEC	blood vessel
17	chr6:12345000-12348600	Weak transcription	Placenta	Placenta
18	chr6:12345400-12347800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:12345800-12347800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:12345800-12348000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:12345800-12348800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:12346200-12348800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:12346400-12348800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:12346400-12348800	Weak transcription	Osteobl	bone
25	chr6:12346600-12348000	Weak transcription	HepG2	liver
26	chr6:12346600-12348800	Weak transcription	Right Atrium	heart
27	chr6:12346800-12347800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:12346800-12348000	Weak transcription	Stomach Mucosa	stomach
29	chr6:12346800-12348600	Weak transcription	Aorta	Aorta
30	chr6:12346800-12348800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:12347000-12348800	Weak transcription	Gastric	stomach
32	chr6:12347000-12348800	Weak transcription	Pancreas	Pancrea

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