Variant report

Variant	rs1790399
Chromosome Location	chr11:73801662-73801663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr11:73801568-73802232	MCF-7	breast:	n/a	n/a
2	MAFK	chr11:73801520-73802122	K562	blood:	n/a	n/a
3	RAD21	chr11:73801631-73802185	A549	lung:	n/a	n/a
4	RAD21	chr11:73801540-73802186	MCF-7	breast:	n/a	n/a
5	RAD21	chr11:73801658-73802193	HCT-116	colon:	n/a	n/a
6	CTCF	chr11:73801636-73802130	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:73780866..73784002-chr11:73798180..73802078,6	MCF-7	breast:
2	chr11:73690232..73696227-chr11:73800984..73805427,5	MCF-7	breast:
3	chr11:73675053..73676351-chr11:73801467..73802637,9	MCF-7	breast:
4	chr11:73800042..73802110-chr11:73880491..73883383,2	MCF-7	breast:
5	chr11:73692520..73695585-chr11:73801085..73803833,3	MCF-7	breast:

No data

Variant related genes	Relation type
C2CD3	TF binding region
ENSG00000255847	Chromatin interaction
ENSG00000187726	Chromatin interaction
ENSG00000214517	Chromatin interaction
ENSG00000168014	Chromatin interaction
ENSG00000175567	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898956	0.82[ASN][1000 genomes]
rs1614299	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1615115	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1685326	0.81[ASN][1000 genomes]
rs1685355	0.87[JPT][hapmap]
rs1726735	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1726744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1726745	0.87[JPT][hapmap]
rs1726746	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1726751	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs1726752	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1726764	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783537	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1790381	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790404	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007567	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2075577	0.87[JPT][hapmap]
rs2848559	0.80[CEU][hapmap]
rs3018184	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4453265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474835	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4944036	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944038	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs500608	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs575096	0.89[EUR][1000 genomes]
rs578057	0.80[CEU][hapmap]
rs588097	0.87[JPT][hapmap]
rs590336	0.87[JPT][hapmap]
rs635441	0.87[JPT][hapmap]
rs647126	0.87[JPT][hapmap]
rs6592545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6592551	0.81[EUR][1000 genomes]
rs7121868	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130095	0.82[YRI][hapmap]
rs7483884	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7926165	0.87[JPT][hapmap]
rs826033	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826039	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826061	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826066	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1790399	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73753200-73804600	Weak transcription	Colonic Mucosa	Colon
2	chr11:73760000-73802600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
5	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:73785600-73803400	Weak transcription	NHDF-Ad	bronchial
7	chr11:73785600-73823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:73787800-73811400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:73794600-73823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:73794800-73804200	Strong transcription	Brain Angular Gyrus	brain
11	chr11:73794800-73805400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:73794800-73806600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:73794800-73806600	Strong transcription	Fetal Lung	lung
14	chr11:73795000-73806000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:73795000-73806000	Strong transcription	Brain Anterior Caudate	brain
16	chr11:73795000-73806400	Strong transcription	Adipose Nuclei	Adipose
17	chr11:73795000-73806600	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:73795000-73808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:73795000-73817400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:73795000-73817600	Strong transcription	Primary B cells from cord blood	blood
21	chr11:73795200-73802400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:73795200-73805000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:73795200-73805800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr11:73795200-73806000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:73795200-73806000	Strong transcription	Placenta	Placenta
26	chr11:73795200-73806400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:73795200-73806400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:73795200-73806400	Strong transcription	HSMMtube	muscle
29	chr11:73795200-73806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:73795200-73807200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr11:73795200-73814600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:73795200-73814600	Strong transcription	Left Ventricle	heart
33	chr11:73795200-73814800	Strong transcription	Liver	Liver
34	chr11:73795200-73815200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr11:73795200-73817600	Strong transcription	Primary T cells from cord blood	blood
36	chr11:73795200-73817600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:73795200-73818200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:73795200-73820600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:73795200-73823800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:73795400-73817800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr11:73795600-73806000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr11:73795800-73806400	Strong transcription	Fetal Brain Female	brain
43	chr11:73795800-73806600	Strong transcription	Hela-S3	cervix
44	chr11:73795800-73815000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:73795800-73817800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr11:73796000-73807600	Strong transcription	Brain Hippocampus Middle	brain
47	chr11:73796000-73817800	Strong transcription	HSMM	muscle
48	chr11:73796400-73802000	Strong transcription	Spleen	Spleen
49	chr11:73796400-73804400	Strong transcription	GM12878-XiMat	blood
50	chr11:73796400-73805600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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