Variant report

Variant	rs2287419
Chromosome Location	chr2:211340678-211340679
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
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	POLR2A	chr2:211340622-211343315	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr2:211340476-211341872	HepG2	liver:	n/a	chr2:211341219-211341229
3	RFX5	chr2:211340284-211342739	SK-N-SH	brain:	n/a	chr2:211341503-211341512
4	MXI1	chr2:211340118-211342969	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:211340153-211341801	GM12891	blood:	n/a	n/a
6	REST	chr2:211340674-211341794	H1-neurons	neurons:	n/a	chr2:211340978-211340986 chr2:211341230-211341240

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:211340637-211340687	AoSMC	blood vessel:	n/a
2	chr2:211340637-211340687	IMR90	lung:	fetal
3	chr2:211340637-211340687	GM12891	blood:	n/a
4	chr2:211340637-211340687	PANC-1	pancreas:	n/a
5	chr2:211340637-211340687	HRE	kidney:	n/a
6	chr2:211340637-211340687	HPAEpiC	pulmonary alveolar:	n/a
7	chr2:211340637-211340687	NH-A	brain:	n/a
8	chr2:211340637-211340687	NHBE	bronchial:	n/a
9	chr2:211340637-211340687	AG09319	gingival:	n/a
10	chr2:211340637-211340687	RPTEC	kidney:	n/a
11	chr2:211340637-211340687	LNCaP	prostate:	n/a
12	chr2:211340637-211340687	AG04449	skin:	fetal
13	chr2:211340637-211340687	SK-N-MC	brain:	n/a
14	chr2:211340637-211340687	HCM	heart:	n/a
15	chr2:211340637-211340687	HUVEC	blood vessel:	n/a
16	chr2:211340637-211340687	HIPEpiC	eye:	n/a
17	chr2:211340637-211340687	HMEC	breast:	n/a
18	chr2:211340637-211340687	BJ	skin:	n/a
19	chr2:211340637-211340687	K562	blood:	n/a
20	chr2:211340637-211340687	MCF-7	breast:	n/a
21	chr2:211340637-211340687	Hepatocyte	liver:	n/a
22	chr2:211340637-211340687	HEK293	kidney:	embryo
23	chr2:211340637-211340687	HCPEpiC	choroid plexus:	n/a
24	chr2:211340637-211340687	AG09309	skin:	n/a
25	chr2:211340637-211340687	GM06990	blood:	n/a
26	chr2:211340637-211340687	HCT-116	colon:	n/a
27	chr2:211340637-211340687	SKMC	muscle:	n/a
28	chr2:211340637-211340687	GM12878	blood:	n/a
29	chr2:211340637-211340687	PrEC	prostate:	n/a
30	chr2:211340637-211340687	HAEpiC	amniotic membrane:	n/a
31	chr2:211340637-211340687	A549	lung:	n/a
32	chr2:211340637-211340687	AG10803	skin:	n/a
33	chr2:211340637-211340687	NHDF-neo	bronchial:	n/a
34	chr2:211340637-211340687	HRPEpiC	eye:	n/a
35	chr2:211340637-211340687	T-47D	breast:	n/a
36	chr2:211340637-211340687	Hela-S3	cervix:	n/a
37	chr2:211340637-211340687	SK-N-SH	brain:	n/a
38	chr2:211340637-211340687	HNPCEpiC	eye:	n/a
39	chr2:211340637-211340687	MCF10A-Er-Src	breast:	n/a
40	chr2:211340637-211340687	BE2_C	brain:	n/a
41	chr2:211340637-211340687	SAEC	small airway:	n/a
42	chr2:211340637-211340687	AG04450	lung:	fetal
43	chr2:211340637-211340687	NB4	blood:	n/a
44	chr2:211340637-211340687	ovcar-3	ovarian:	n/a
45	chr2:211340637-211340687	HL-60	blood:	n/a
46	chr2:211340637-211340687	ECC-1	luminal epithelium:	n/a
47	chr2:211340637-211340687	HepG2	liver:	n/a
48	chr2:211340637-211340687	Jurkat	blood:	n/a
49	chr2:211340637-211340687	HCF	heart:	n/a
50	chr2:211340637-211340687	CMK	blood:	n/a

No data

Variant related genes	Relation type
CPS1	TF binding region
CPS1	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10932334	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474078	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618926	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623942	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1396954	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17552879	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042049	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287418	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287421	0.99[ASN][1000 genomes]
rs2287422	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2370948	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732055	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770685	0.99[ASN][1000 genomes]
rs3770687	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770690	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770691	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856340	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856342	0.97[ASN][1000 genomes]
rs3856343	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856344	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856345	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856346	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856347	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856349	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4672575	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4672577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4673530	0.99[ASN][1000 genomes]
rs4673531	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4673532	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4673533	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203668	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203669	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203670	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203674	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6727682	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7569252	0.85[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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2287419	CPS1	cis	Adipose Subcutaneous	GTEx
rs2287419	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs2287419	CPS1	cis	lung	GTEx
rs2287419	CPS1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:211325800-211340800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:211331400-211341000	Weak transcription	Spleen	Spleen
5	chr2:211332000-211340800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:211333600-211340800	Weak transcription	Esophagus	oesophagus
7	chr2:211333600-211340800	Weak transcription	Lung	lung
8	chr2:211333600-211340800	Weak transcription	Pancreas	Pancrea
9	chr2:211333600-211341000	Weak transcription	Gastric	stomach
10	chr2:211335200-211340800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:211336800-211340800	Weak transcription	Placenta	Placenta
12	chr2:211336800-211340800	Weak transcription	Left Ventricle	heart
13	chr2:211338200-211341000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:211339600-211340800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:211339800-211342000	Active TSS	Brain Substantia Nigra	brain
16	chr2:211339800-211342600	Active TSS	Brain Angular Gyrus	brain
17	chr2:211339800-211342800	Active TSS	A549	lung
18	chr2:211340000-211340800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:211340000-211342800	Active TSS	Brain Anterior Caudate	brain
20	chr2:211340200-211340800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:211340200-211340800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:211340200-211340800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr2:211340200-211340800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:211340200-211340800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr2:211340200-211340800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:211340200-211340800	Enhancers	Small Intestine	intestine
27	chr2:211340200-211340800	Flanking Active TSS	NHEK	skin
28	chr2:211340200-211341000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:211340200-211341000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:211340200-211341200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:211340200-211341800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:211340200-211341800	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:211340200-211342000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:211340200-211342600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:211340200-211342600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:211340200-211342800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:211340200-211342800	Active TSS	Hela-S3	cervix
38	chr2:211340200-211343000	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:211340200-211343000	Active TSS	HSMMtube	muscle
40	chr2:211340200-211343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:211340400-211340800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:211340400-211340800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr2:211340400-211340800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:211340400-211340800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:211340400-211340800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:211340400-211340800	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr2:211340400-211340800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:211340400-211340800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:211340400-211340800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:211340400-211340800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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