Variant report

Variant	rs3754209
Chromosome Location	chr1:150604110-150604111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150604017-150604227	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150600620..150604710-chr1:150667156..150670884,6	K562	blood:
2	chr1:150600086..150604497-chr1:150798595..150803015,4	MCF-7	breast:
3	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
4	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:
5	chr1:150548752..150555486-chr1:150599368..150605834,15	MCF-7	breast:
6	chr1:150547986..150553838-chr1:150598744..150606232,19	K562	blood:
7	chr1:150602761..150604761-chr1:150618641..150620910,2	MCF-7	breast:
8	chr1:150602963..150605851-chr1:150608537..150610642,4	K562	blood:
9	chr1:150534063..150535879-chr1:150604079..150606306,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTSL4-7	chr1:150602100-150609632	NONHSAT006322

No data

Variant related genes	Relation type
ENSA	TF binding region
ENSG00000264508	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143457	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1053732	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888384	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888385	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204668	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11204669	0.80[ASN][1000 genomes]
rs11204675	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204677	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204678	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204679	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204680	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585169	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12125672	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126271	0.83[ASN][1000 genomes]
rs12139563	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12406712	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12746899	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1971378	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048558	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738484	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738485	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970918	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970923	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971041	0.84[AFR][1000 genomes]
rs55862611	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61820165	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669122	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697620	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6698495	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878471	0.81[ASN][1000 genomes]
rs9803935	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3754209	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs3754209	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs3754209	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs3754209	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs3754209	ARNT	cis	Thyroid	GTEx
rs3754209	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs3754209	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs3754209	CTSS	cis	Nerve Tibial	GTEx
rs3754209	HORMAD1	cis	Esophagus Mucosa	GTEx
rs3754209	HORMAD1	cis	Nerve Tibial	GTEx
rs3754209	GOLPH3L	cis	Nerve Tibial	GTEx
rs3754209	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs3754209	RNU6-1042P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150600600-150604200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:150601200-150604400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:150602600-150607200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:150602600-150608000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:150603000-150607800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:150603000-150608000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:150603000-150608200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:150603000-150619000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:150603000-150619600	Weak transcription	Small Intestine	intestine
10	chr1:150603200-150604200	Enhancers	Right Atrium	heart
11	chr1:150603200-150604600	Weak transcription	Fetal Heart	heart
12	chr1:150603200-150607200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:150603200-150607200	Weak transcription	HepG2	liver
14	chr1:150603200-150607600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:150603200-150607600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:150603200-150607600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:150603200-150607800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:150603200-150608000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:150603200-150608200	Weak transcription	Stomach Mucosa	stomach
20	chr1:150603200-150608200	Weak transcription	Hela-S3	cervix
21	chr1:150603200-150616600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:150603200-150617400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:150603200-150618600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:150603200-150619600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:150603200-150619600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:150603200-150619600	Weak transcription	Fetal Stomach	stomach
27	chr1:150603200-150619800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:150603200-150620000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:150603200-150620000	Weak transcription	Gastric	stomach
30	chr1:150603200-150620000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:150603200-150620600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:150603200-150620600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:150603200-150661200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:150603400-150604200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:150603400-150604200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:150603400-150604400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:150603400-150606600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:150603400-150607200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:150603400-150607200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:150603400-150608000	Weak transcription	Placenta	Placenta
41	chr1:150603400-150616800	Weak transcription	Liver	Liver
42	chr1:150603400-150618000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:150603400-150618200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:150603400-150618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:150603400-150618200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:150603400-150618800	Weak transcription	Osteobl	bone
47	chr1:150603400-150619000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:150603400-150620000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:150603400-150620400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:150603400-150620600	Weak transcription	Right Ventricle	heart

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