Variant report

Variant	rs4946976
Chromosome Location	chr6:109772518-109772519
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	chr6:109770371..109773024-chr6:109807786..109809712,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223537	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1046943	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1074765	0.88[EUR][1000 genomes]
rs1074766	0.86[EUR][1000 genomes]
rs10872033	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11251	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214147	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12529733	0.83[EUR][1000 genomes]
rs13219952	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1476387	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1521907	0.88[EUR][1000 genomes]
rs17070591	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1885690	0.88[EUR][1000 genomes]
rs1885691	0.89[EUR][1000 genomes]
rs1998811	0.84[EUR][1000 genomes]
rs2211288	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2236084	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2277113	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2884037	0.88[EUR][1000 genomes]
rs35146243	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35260632	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3734652	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3757230	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3757231	0.89[EUR][1000 genomes]
rs3757235	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3778474	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3778478	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3799842	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3818933	0.88[EUR][1000 genomes]
rs4636056	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4945831	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946967	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4946970	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs58644322	0.88[EUR][1000 genomes]
rs59597139	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6914216	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920372	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6939548	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6939953	0.88[EUR][1000 genomes]
rs699700	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs730089	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs736830	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs746794	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7748669	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7751582	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7754650	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755941	0.82[EUR][1000 genomes]
rs7768973	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7773950	0.82[EUR][1000 genomes]
rs8465	0.88[EUR][1000 genomes]
rs910730	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320286	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9398202	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9480947	0.90[EUR][1000 genomes]
rs9480949	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9480956	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9480958	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487064	0.82[EUR][1000 genomes]
rs9487066	0.81[EUR][1000 genomes]
rs9487069	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9487070	0.88[EUR][1000 genomes]
rs9487076	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9487084	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9487085	0.88[EUR][1000 genomes]
rs9487103	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs974034	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9791241	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4946976	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs4946976	RP11-425D10.10	cis	Whole Blood	GTEx
rs4946976	SMPD2	cis	Esophagus Mucosa	GTEx
rs4946976	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4946976	MICAL1	cis	Artery Tibial	GTEx
rs4946976	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	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	chr6:109763600-109773200	Weak transcription	Fetal Brain Male	brain
8	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
11	chr6:109763800-109774400	Strong transcription	HSMM	muscle
12	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
14	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
15	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:109763800-109775600	Weak transcription	HepG2	liver
18	chr6:109764000-109774400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr6:109764000-109774600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:109764000-109774800	Strong transcription	Fetal Intestine Large	intestine
21	chr6:109764000-109775000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:109764200-109774600	Strong transcription	Brain Germinal Matrix	brain
23	chr6:109764200-109774600	Weak transcription	Stomach Mucosa	stomach
24	chr6:109764200-109774800	Strong transcription	Fetal Brain Female	brain
25	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
26	chr6:109765400-109773600	Strong transcription	NHDF-Ad	bronchial
27	chr6:109765400-109773800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:109766800-109773200	Weak transcription	NH-A	brain
30	chr6:109766800-109775200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:109767000-109776000	Weak transcription	A549	lung
33	chr6:109767200-109776000	Weak transcription	Osteobl	bone
34	chr6:109767400-109774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:109767800-109773000	Weak transcription	HMEC	breast
36	chr6:109768000-109772800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:109768200-109772600	Weak transcription	Fetal Lung	lung
38	chr6:109768200-109772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:109768200-109774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:109768400-109772800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:109768400-109772800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:109768400-109773000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:109768400-109775800	Weak transcription	Liver	Liver
44	chr6:109768400-109775800	Weak transcription	Left Ventricle	heart
45	chr6:109768400-109776000	Weak transcription	Ovary	ovary
46	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:109768400-109776400	Weak transcription	K562	blood
48	chr6:109768600-109772600	Weak transcription	Right Ventricle	heart
49	chr6:109768600-109772800	Weak transcription	Adipose Nuclei	Adipose
50	chr6:109768800-109772800	Weak transcription	H1 Cell Line	embryonic stem cell

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