Variant report

Variant	rs3778478
Chromosome Location	chr6:109791630-109791631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109791600-109792947	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:109791416-109791695	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109764609..109767226-chr6:109791352..109794243,2	K562	blood:
2	chr6:109785460..109788370-chr6:109788887..109793014,3	K562	blood:
3	chr6:109760223..109762958-chr6:109790032..109792982,2	K562	blood:
4	chr6:109786175..109787997-chr6:109790451..109793066,2	K562	blood:
5	chr6:109789452..109792646-chr6:109795758..109798089,3	K562	blood:

No data

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000135587	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10457192	0.83[EUR][1000 genomes]
rs10457194	0.83[EUR][1000 genomes]
rs1046943	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054607	0.92[ASN][1000 genomes]
rs1074765	0.87[EUR][1000 genomes]
rs1074766	0.85[EUR][1000 genomes]
rs10872033	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11153183	0.83[EUR][1000 genomes]
rs11251	0.86[EUR][1000 genomes]
rs11754455	0.83[EUR][1000 genomes]
rs12197180	0.83[EUR][1000 genomes]
rs12198938	0.83[EUR][1000 genomes]
rs12199154	0.83[EUR][1000 genomes]
rs12212476	0.83[EUR][1000 genomes]
rs12214147	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12529733	0.81[EUR][1000 genomes]
rs13201430	0.86[ASN][1000 genomes]
rs13203587	0.83[EUR][1000 genomes]
rs13219952	0.86[EUR][1000 genomes]
rs13220915	0.83[EUR][1000 genomes]
rs1406899	0.83[EUR][1000 genomes]
rs1476387	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1476388	0.81[EUR][1000 genomes]
rs1521907	0.86[EUR][1000 genomes]
rs17070591	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1885690	0.86[EUR][1000 genomes]
rs1885691	0.88[EUR][1000 genomes]
rs1998811	0.87[EUR][1000 genomes]
rs2024849	0.83[EUR][1000 genomes]
rs2024850	0.83[EUR][1000 genomes]
rs2024852	0.83[EUR][1000 genomes]
rs2024853	0.83[EUR][1000 genomes]
rs2211288	0.88[EUR][1000 genomes]
rs2236084	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277113	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277114	0.83[EUR][1000 genomes]
rs2884037	0.86[EUR][1000 genomes]
rs35146243	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35260632	0.88[AMR][1000 genomes]
rs3734652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757230	0.87[EUR][1000 genomes]
rs3757231	0.88[EUR][1000 genomes]
rs3757235	0.88[EUR][1000 genomes]
rs3778474	0.86[EUR][1000 genomes]
rs3799842	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818933	0.87[EUR][1000 genomes]
rs4636056	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4945831	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4946967	0.86[EUR][1000 genomes]
rs4946970	0.88[EUR][1000 genomes]
rs4946976	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58644322	0.86[EUR][1000 genomes]
rs59597139	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911838	0.85[ASN][1000 genomes]
rs6914216	0.86[EUR][1000 genomes]
rs6920372	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6920712	0.92[ASN][1000 genomes]
rs6939548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939953	0.86[EUR][1000 genomes]
rs699700	0.86[EUR][1000 genomes]
rs730089	0.88[EUR][1000 genomes]
rs736830	0.88[EUR][1000 genomes]
rs746794	0.88[EUR][1000 genomes]
rs7748669	0.90[EUR][1000 genomes]
rs7751582	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7754650	0.88[EUR][1000 genomes]
rs7755941	0.85[EUR][1000 genomes]
rs7768973	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7773950	0.85[EUR][1000 genomes]
rs8465	0.87[EUR][1000 genomes]
rs910730	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9320286	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9398202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9400284	0.87[ASN][1000 genomes]
rs9400287	0.83[ASN][1000 genomes]
rs9480947	0.88[EUR][1000 genomes]
rs9480949	0.87[EUR][1000 genomes]
rs9480956	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9480958	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9487064	0.81[EUR][1000 genomes]
rs9487069	0.86[EUR][1000 genomes]
rs9487070	0.87[EUR][1000 genomes]
rs9487076	0.87[EUR][1000 genomes]
rs9487084	0.88[EUR][1000 genomes]
rs9487085	0.86[EUR][1000 genomes]
rs9487103	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs974034	0.87[EUR][1000 genomes]
rs9791241	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3778478	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3778478	MICAL1	cis	Artery Tibial	GTEx
rs3778478	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3778478	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs3778478	SMPD2	cis	Esophagus Mucosa	GTEx
rs3778478	RP11-425D10.10	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109778800-109798800	Weak transcription	Small Intestine	intestine
2	chr6:109780600-109800400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:109781400-109802200	Strong transcription	HSMM	muscle
4	chr6:109782000-109798800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:109782000-109799000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:109782200-109792400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:109782400-109797600	Strong transcription	Dnd41	blood
8	chr6:109782400-109797800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:109782400-109798000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:109782400-109798200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:109782400-109798800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:109782400-109798800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:109782400-109798800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:109782400-109798800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:109782400-109799000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:109782400-109799000	Strong transcription	Placenta	Placenta
17	chr6:109782400-109799200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:109782400-109799800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:109782400-109799800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:109782400-109800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:109782400-109803000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:109782600-109797800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:109782600-109799600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr6:109782600-109800000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:109782800-109792600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr6:109783000-109797800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:109783000-109798000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:109783000-109798200	Strong transcription	Adipose Nuclei	Adipose
29	chr6:109783200-109799800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:109783600-109799000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:109785000-109794000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:109785200-109794800	Strong transcription	HMEC	breast
33	chr6:109785200-109796800	Strong transcription	Liver	Liver
34	chr6:109785600-109797800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:109785600-109798200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:109785600-109799200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:109785800-109793200	Strong transcription	A549	lung
38	chr6:109785800-109796400	Strong transcription	Primary T cells from cord blood	blood
39	chr6:109785800-109798800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:109786000-109793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:109786000-109794600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:109786000-109797800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:109786200-109797000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:109786200-109797600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:109786200-109798200	Strong transcription	Osteobl	bone
46	chr6:109786200-109800200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:109786400-109792200	Strong transcription	GM12878-XiMat	blood
48	chr6:109786400-109799600	Strong transcription	Fetal Muscle Leg	muscle
49	chr6:109786600-109795000	Strong transcription	NHEK	skin
50	chr6:109786600-109799200	Strong transcription	Fetal Stomach	stomach

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