Variant report

Variant	rs2287417
Chromosome Location	chr2:211341599-211341600
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:211341059-211341760	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:211341134-211341630	U87	brain:	n/a	n/a
3	SP1	chr2:211341055-211341770	A549	lung:	n/a	chr2:211341530-211341542 chr2:211341530-211341542 chr2:211341531-211341540 chr2:211341531-211341541
4	RCOR1	chr2:211341287-211341621	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:211341043-211341708	ProgFib	skin:	n/a	n/a
6	POLR2A	chr2:211340622-211343315	MCF10A-Er-Src	breast:	n/a	n/a
7	RFX5	chr2:211341242-211341614	GM12878	blood:	n/a	chr2:211341503-211341512
8	TBP	chr2:211341232-211341717	GM12878	blood:	n/a	n/a
9	MAFK	chr2:211340956-211341712	Hela-S3	cervix:	n/a	n/a
10	GTF2F1	chr2:211341266-211341617	Hela-S3	cervix:	n/a	n/a
11	MAX	chr2:211341004-211341791	NB4	blood:	n/a	chr2:211341219-211341229
12	SP1	chr2:211341279-211341671	GM12878	blood:	n/a	chr2:211341530-211341542 chr2:211341530-211341542 chr2:211341531-211341540 chr2:211341531-211341541
13	IRF1	chr2:211340972-211341734	K562	blood:	n/a	chr2:211341152-211341166 chr2:211341152-211341162 chr2:211341153-211341164 chr2:211341528-211341542 chr2:211341150-211341164
14	MXI1	chr2:211341035-211341655	HepG2	liver:	n/a	n/a
15	MYC	chr2:211341400-211341601	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF12	chr2:211341055-211341608	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:211341108-211341673	GM15510	blood:	n/a	n/a
18	MTA3	chr2:211340860-211341675	GM12878	blood:	n/a	n/a
19	GABPA	chr2:211341133-211341746	A549	lung:	n/a	n/a
20	MAX	chr2:211340476-211341872	HepG2	liver:	n/a	chr2:211341219-211341229
21	MAX	chr2:211341192-211341638	Hela-S3	cervix:	n/a	chr2:211341219-211341229
22	SP1	chr2:211340996-211341816	HCT-116	colon:	n/a	chr2:211341530-211341542 chr2:211340999-211341013 chr2:211341530-211341542 chr2:211341531-211341540 chr2:211341531-211341541
23	POLR2A	chr2:211341048-211341687	MCF-7	breast:	n/a	n/a
24	ETS1	chr2:211341240-211341640	A549	lung:	n/a	n/a
25	HDAC2	chr2:211341141-211341653	HepG2	liver:	n/a	n/a
26	SPI1	chr2:211341340-211341636	GM12891	blood:	n/a	n/a
27	POLR2A	chr2:211340967-211341706	HepG2	liver:	n/a	n/a
28	GABPA	chr2:211341290-211341624	A549	lung:	n/a	n/a
29	SP1	chr2:211341216-211341684	H1-hESC	embryonic stem cell:	n/a	chr2:211341530-211341542 chr2:211341530-211341542 chr2:211341531-211341540 chr2:211341531-211341541
30	REST	chr2:211340967-211341639	HepG2	liver:	n/a	chr2:211340978-211340986 chr2:211341230-211341240
31	POLR2A	chr2:211341180-211341663	K562	blood:	n/a	n/a
32	TAF1	chr2:211340895-211341647	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:211341227-211341788	SK-N-SH	brain:	n/a	n/a
34	MAX	chr2:211341144-211341636	K562	blood:	n/a	chr2:211341219-211341229
35	MYC	chr2:211341006-211341656	NB4	blood:	n/a	chr2:211341219-211341229
36	POLR2A	chr2:211341069-211341740	HL-60	blood:	n/a	n/a
37	TBP	chr2:211341005-211341662	HepG2	liver:	n/a	n/a
38	MXI1	chr2:211341180-211341770	GM12878	blood:	n/a	n/a
39	E2F6	chr2:211341154-211341778	A549	lung:	n/a	chr2:211341198-211341208 chr2:211341502-211341511
40	HCFC1	chr2:211340908-211341769	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr2:211341157-211341607	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:211341145-211341723	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr2:211341173-211341677	K562	blood:	n/a	n/a
44	RCOR1	chr2:211340837-211341821	IMR90	lung:	n/a	n/a
45	UBTF	chr2:211340997-211341604	K562	blood:	n/a	n/a
46	STAT1	chr2:211341277-211341712	GM12878	blood:	n/a	n/a
47	MAZ	chr2:211341107-211341653	HepG2	liver:	n/a	chr2:211341219-211341229
48	RFX5	chr2:211340284-211342739	SK-N-SH	brain:	n/a	chr2:211341503-211341512
49	POLR2A	chr2:211341135-211341639	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:211341010-211341708	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:211341572-211341622	SKMC	muscle:	n/a
2	chr2:211341572-211341622	NT2-D1	testis:	n/a
3	chr2:211341572-211341622	U87	brain:	n/a
4	chr2:211341572-211341622	HRPEpiC	eye:	n/a
5	chr2:211341572-211341622	PrEC	prostate:	n/a
6	chr2:211341572-211341622	HRE	kidney:	n/a
7	chr2:211341572-211341622	GM06990	blood:	n/a
8	chr2:211341572-211341622	GM19239	blood:	n/a
9	chr2:211341572-211341622	HepG2	liver:	n/a
10	chr2:211341572-211341622	NB4	blood:	n/a
11	chr2:211341572-211341622	BE2_C	brain:	n/a
12	chr2:211341572-211341622	LNCaP	prostate:	n/a
13	chr2:211341572-211341622	HUVEC	blood vessel:	n/a
14	chr2:211341572-211341622	AoSMC	blood vessel:	n/a
15	chr2:211341572-211341622	GM12892	blood:	n/a
16	chr2:211341572-211341622	CMK	blood:	n/a
17	chr2:211341572-211341622	AG10803	skin:	n/a
18	chr2:211341572-211341622	HCT-116	colon:	n/a
19	chr2:211341572-211341622	HL-60	blood:	n/a
20	chr2:211341572-211341622	A549	lung:	n/a
21	chr2:211341572-211341622	ECC-1	luminal epithelium:	n/a
22	chr2:211341572-211341622	Hepatocyte	liver:	n/a
23	chr2:211341572-211341622	AG09319	gingival:	n/a
24	chr2:211341572-211341622	BJ	skin:	n/a
25	chr2:211341572-211341622	HPAEpiC	pulmonary alveolar:	n/a
26	chr2:211341572-211341622	Hela-S3	cervix:	n/a
27	chr2:211341572-211341622	PANC-1	pancreas:	n/a
28	chr2:211341572-211341622	IMR90	lung:	fetal
29	chr2:211341572-211341622	HIPEpiC	eye:	n/a
30	chr2:211341572-211341622	HCM	heart:	n/a
31	chr2:211341572-211341622	NH-A	brain:	n/a
32	chr2:211341572-211341622	SK-N-SH	brain:	n/a
33	chr2:211341572-211341622	MCF-7	breast:	n/a
34	chr2:211341572-211341622	H1-hESC	embryonic stem cell:	embryo
35	chr2:211341572-211341622	ProgFib	skin:	n/a
36	chr2:211341572-211341622	AG04450	lung:	fetal
37	chr2:211341572-211341622	AG09309	skin:	n/a
38	chr2:211341572-211341622	HCF	heart:	n/a
39	chr2:211341572-211341622	HMEC	breast:	n/a
40	chr2:211341572-211341622	ovcar-3	ovarian:	n/a
41	chr2:211341572-211341622	HEK293	kidney:	embryo
42	chr2:211341572-211341622	T-47D	breast:	n/a
43	chr2:211341572-211341622	HCPEpiC	choroid plexus:	n/a
44	chr2:211341572-211341622	Caco-2	colon:	n/a
45	chr2:211341572-211341622	NHDF-neo	bronchial:	n/a
46	chr2:211341572-211341622	Jurkat	blood:	n/a
47	chr2:211341572-211341622	SAEC	small airway:	n/a
48	chr2:211341572-211341622	SK-N-SH_RA	brain:	n/a
49	chr2:211341572-211341622	HRCEpiC	kidney:	n/a
50	chr2:211341572-211341622	K562	blood:	n/a

Variant related genes	Relation type
CPS1	TF binding region
LANCL1	TF binding region
CPS1	CpG island
LANCL1	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474078	0.97[AMR][1000 genomes];0.86[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];0.96[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];1.00[ASN][1000 genomes]
rs2042049	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287418	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.93[ASN][1000 genomes]
rs3755182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770685	0.99[ASN][1000 genomes]
rs3770687	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[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	0.98[ASN][1000 genomes]
rs3856343	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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];0.98[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];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856349	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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];0.97[ASN][1000 genomes]
rs4673530	0.99[ASN][1000 genomes]
rs4673531	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4673532	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4673533	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203668	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203669	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203670	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203674	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62203675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727682	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7569252	0.84[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
rs2287417	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs2287417	CPS1	cis	lung	GTEx
rs2287417	CPS1	cis	Artery Tibial	GTEx
rs2287417	CPS1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211339800-211342000	Active TSS	Brain Substantia Nigra	brain
2	chr2:211339800-211342600	Active TSS	Brain Angular Gyrus	brain
3	chr2:211339800-211342800	Active TSS	A549	lung
4	chr2:211340000-211342800	Active TSS	Brain Anterior Caudate	brain
5	chr2:211340200-211341800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:211340200-211341800	Active TSS	Fetal Muscle Trunk	muscle
7	chr2:211340200-211342000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:211340200-211342600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:211340200-211342600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:211340200-211342800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:211340200-211342800	Active TSS	Hela-S3	cervix
12	chr2:211340200-211343000	Active TSS	Stomach Smooth Muscle	stomach
13	chr2:211340200-211343000	Active TSS	HSMMtube	muscle
14	chr2:211340200-211343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:211340400-211341600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:211340400-211341600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:211340400-211341600	Active TSS	Fetal Brain Male	brain
18	chr2:211340400-211341800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:211340400-211341800	Active TSS	Fetal Kidney	kidney
20	chr2:211340400-211342000	Active TSS	Fetal Brain Female	brain
21	chr2:211340400-211342000	Active TSS	Thymus	Thymus
22	chr2:211340400-211342400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:211340400-211342400	Active TSS	Brain Cingulate Gyrus	brain
24	chr2:211340400-211342400	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr2:211340400-211342600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr2:211340400-211342600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr2:211340400-211342600	Active TSS	Right Ventricle	heart
28	chr2:211340400-211342800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr2:211340400-211342800	Active TSS	Aorta	Aorta
30	chr2:211340400-211342800	Active TSS	NHDF-Ad	bronchial
31	chr2:211340400-211343000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:211340400-211343000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:211340400-211343000	Active TSS	Right Atrium	heart
34	chr2:211340400-211343000	Active TSS	GM12878-XiMat	blood
35	chr2:211340400-211343000	Active TSS	HSMM	muscle
36	chr2:211340400-211343200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:211340400-211343200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:211340400-211343200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:211340400-211343200	Active TSS	Ovary	ovary
40	chr2:211340400-211343200	Active TSS	NHLF	lung
41	chr2:211340400-211343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:211340600-211341600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr2:211340600-211341600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:211340600-211341600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr2:211340600-211341600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr2:211340600-211341800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr2:211340600-211341800	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr2:211340600-211341800	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:211340600-211341800	Active TSS	Brain Germinal Matrix	brain
50	chr2:211340600-211341800	Active TSS	Colonic Mucosa	Colon

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