Variant report

Variant	rs2327544
Chromosome Location	chr6:12345969-12345970
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	chr6:12324741..12326654-chr6:12344766..12346317,2	MCF-7	breast:
2	chr6:12341804..12346306-chr6:12347487..12351106,5	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10807258	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095344	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184329	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4379286	0.85[GIH][hapmap]
rs9369262	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs9381035	0.82[MEX][hapmap]
rs9462681	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9462684	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9471538	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2327544	TMEM116	trans	cerebellum	SCAN
rs2327544	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 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	chr6:12339000-12346200	Enhancers	Fetal Intestine Large	intestine
3	chr6:12340800-12348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:12341000-12348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:12341600-12346800	Enhancers	Stomach Mucosa	stomach
6	chr6:12342000-12347000	Enhancers	Pancreas	Pancrea
7	chr6:12342600-12346600	Weak transcription	Gastric	stomach
8	chr6:12343200-12348800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:12343200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:12343200-12351400	Weak transcription	Colonic Mucosa	Colon
11	chr6:12344200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:12344400-12346000	Enhancers	HepG2	liver
13	chr6:12344400-12348600	Weak transcription	NHEK	skin
14	chr6:12344400-12348800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:12344400-12348800	Weak transcription	NH-A	brain
16	chr6:12344600-12348600	Weak transcription	Hela-S3	cervix
17	chr6:12344600-12348800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:12344600-12349200	Enhancers	A549	lung
19	chr6:12344600-12349800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:12344800-12348600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:12344800-12348600	Weak transcription	HUVEC	blood vessel
22	chr6:12345000-12346200	Weak transcription	Aorta	Aorta
23	chr6:12345000-12348600	Weak transcription	Placenta	Placenta
24	chr6:12345400-12346400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:12345400-12346400	Enhancers	Osteobl	bone
26	chr6:12345400-12347800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:12345600-12346200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:12345600-12346400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:12345600-12346800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:12345800-12346200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:12345800-12346400	Weak transcription	Right Atrium	heart
32	chr6:12345800-12347800	Weak transcription	Fetal Intestine Small	intestine
33	chr6:12345800-12348000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:12345800-12348800	Weak transcription	Duodenum Mucosa	Duodenum

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