Variant report

Variant	rs1546980
Chromosome Location	chr6:109773946-109773947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109773886-109774032	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:109773258-109774006	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:109772754-109774101	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109752135..109753752-chr6:109773019..109775063,2	K562	blood:

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10080429	0.89[EUR][1000 genomes]
rs1040284	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10457190	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457192	0.84[ASN][1000 genomes]
rs10457194	0.81[ASN][1000 genomes]
rs1048203	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782161	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782162	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782163	0.83[ASN][1000 genomes]
rs10872032	0.86[EUR][1000 genomes]
rs10872034	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153174	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153175	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153176	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153177	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11153180	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11153181	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11153183	0.84[ASN][1000 genomes]
rs11754455	0.84[ASN][1000 genomes]
rs11967108	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190920	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12190996	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192847	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193493	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12197114	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12197180	0.82[ASN][1000 genomes]
rs12198938	0.84[ASN][1000 genomes]
rs12199154	0.84[ASN][1000 genomes]
rs12206928	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12209691	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12212476	0.84[ASN][1000 genomes]
rs12213313	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12524273	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12524639	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528822	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13201951	0.81[ASN][1000 genomes]
rs13203587	0.84[ASN][1000 genomes]
rs13212766	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13220915	0.84[ASN][1000 genomes]
rs1322816	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1358997	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1358998	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1406899	0.84[ASN][1000 genomes]
rs1476388	0.83[ASN][1000 genomes]
rs1590306	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17070580	0.89[EUR][1000 genomes]
rs1923725	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1998811	0.84[ASN][1000 genomes]
rs2024849	0.84[ASN][1000 genomes]
rs2024850	0.84[ASN][1000 genomes]
rs2024852	0.84[ASN][1000 genomes]
rs2024853	0.84[ASN][1000 genomes]
rs2236582	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275650	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2277114	0.84[ASN][1000 genomes]
rs34202013	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35056702	0.89[EUR][1000 genomes]
rs36035949	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36099706	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757234	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778475	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799839	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807005	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818934	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59056467	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59906308	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68042406	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6906216	0.82[ASN][1000 genomes]
rs6911838	0.90[EUR][1000 genomes]
rs6916579	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926096	0.82[ASN][1000 genomes]
rs6929023	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7372	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs749517	0.83[ASN][1000 genomes]
rs752262	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7755941	0.84[ASN][1000 genomes]
rs7773095	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7773950	0.84[ASN][1000 genomes]
rs9320287	0.89[EUR][1000 genomes]
rs9480933	0.85[EUR][1000 genomes]
rs9480948	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480951	0.89[EUR][1000 genomes]
rs9480953	0.89[EUR][1000 genomes]
rs9480955	0.89[EUR][1000 genomes]
rs9480957	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9487068	0.88[EUR][1000 genomes]
rs9487094	0.89[EUR][1000 genomes]
rs9487095	0.89[EUR][1000 genomes]
rs9487097	0.86[EUR][1000 genomes]
rs9487098	0.86[EUR][1000 genomes]
rs9487100	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9885646	0.89[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1546980	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs1546980	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs1546980	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs1546980	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs1546980	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
4	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
5	chr6:109763400-109775000	Strong transcription	NHLF	lung
6	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
10	chr6:109763800-109774400	Strong transcription	HSMM	muscle
11	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
13	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
14	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:109763800-109775600	Weak transcription	HepG2	liver
17	chr6:109764000-109774400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr6:109764000-109774600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:109764000-109774800	Strong transcription	Fetal Intestine Large	intestine
20	chr6:109764000-109775000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:109764200-109774600	Strong transcription	Brain Germinal Matrix	brain
22	chr6:109764200-109774600	Weak transcription	Stomach Mucosa	stomach
23	chr6:109764200-109774800	Strong transcription	Fetal Brain Female	brain
24	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
25	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:109766800-109775200	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:109767000-109776000	Weak transcription	A549	lung
29	chr6:109767200-109776000	Weak transcription	Osteobl	bone
30	chr6:109767400-109774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:109768200-109774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:109768400-109775800	Weak transcription	Liver	Liver
33	chr6:109768400-109775800	Weak transcription	Left Ventricle	heart
34	chr6:109768400-109776000	Weak transcription	Ovary	ovary
35	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:109768400-109776400	Weak transcription	K562	blood
37	chr6:109768800-109774400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:109769000-109774800	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr6:109769000-109775200	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr6:109769000-109775200	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr6:109769400-109774600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr6:109770600-109775000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:109770600-109775000	Weak transcription	Brain Angular Gyrus	brain
44	chr6:109770600-109775200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:109770600-109775400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:109770800-109774800	Weak transcription	Pancreas	Pancrea
47	chr6:109770800-109775200	Weak transcription	Brain Substantia Nigra	brain
48	chr6:109771200-109774800	Genic enhancers	GM12878-XiMat	blood
49	chr6:109771200-109775000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
50	chr6:109771400-109774400	Strong transcription	Fetal Intestine Small	intestine

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