Variant report

Variant	rs10807258
Chromosome Location	chr6:12344262-12344263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12288501..12289080-chr6:12343666..12344460,2	MCF-7	breast:
2	chr6:12341804..12346306-chr6:12347487..12351106,5	MCF-7	breast:
3	chr6:12343799..12344581-chr6:12371956..12372456,2	MCF-7	breast:
4	chr6:12288259..12289080-chr6:12343666..12344329,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2095344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095345	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2184329	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2327544	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4379286	0.83[GIH][hapmap]
rs9369262	0.87[GIH][hapmap];0.82[TSI][hapmap]
rs9462681	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9462684	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9471538	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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
rs10807258	TMEM116	trans	cerebellum	SCAN
rs10807258	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:37 , 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	chr6:12338200-12345800	Enhancers	Fetal Intestine Small	intestine
3	chr6:12338800-12345800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:12339000-12346200	Enhancers	Fetal Intestine Large	intestine
5	chr6:12340800-12348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:12341000-12348000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:12341600-12344800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr6:12341600-12345800	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:12341600-12346800	Enhancers	Stomach Mucosa	stomach
10	chr6:12341800-12344400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:12342000-12344400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:12342000-12344600	Enhancers	Hela-S3	cervix
13	chr6:12342000-12347000	Enhancers	Pancreas	Pancrea
14	chr6:12342600-12346600	Weak transcription	Gastric	stomach
15	chr6:12343000-12344800	Flanking Active TSS	Liver	Liver
16	chr6:12343200-12348800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:12343200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:12343200-12351400	Weak transcription	Colonic Mucosa	Colon
19	chr6:12343400-12344400	Enhancers	NHEK	skin
20	chr6:12343400-12344800	Enhancers	Fetal Kidney	kidney
21	chr6:12343400-12344800	Enhancers	HUVEC	blood vessel
22	chr6:12343600-12344400	Flanking Active TSS	HepG2	liver
23	chr6:12343600-12344600	Enhancers	Lung	lung
24	chr6:12343600-12344600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr6:12343600-12345400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:12343800-12344400	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:12343800-12344400	Enhancers	NH-A	brain
28	chr6:12343800-12345000	Enhancers	Placenta	Placenta
29	chr6:12343800-12345200	Enhancers	Small Intestine	intestine
30	chr6:12343800-12345400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:12344000-12344400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:12344000-12344600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:12344000-12345000	Enhancers	Aorta	Aorta
34	chr6:12344000-12345400	Weak transcription	Osteobl	bone
35	chr6:12344200-12344400	Enhancers	A549	lung
36	chr6:12344200-12345600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:12344200-12348800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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