Variant report

Variant	rs12464878
Chromosome Location	chr2:211342925-211342926
allele	C/T
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	chr2:211340622-211343315	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr2:211342182-211342961	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr2:211340118-211342969	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LANCL1	TF binding region

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];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];0.95[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];0.99[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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.86[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];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856344	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856345	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856346	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856347	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856349	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672575	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4672577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4673530	0.99[ASN][1000 genomes]
rs4673531	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4673532	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4673533	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203668	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203669	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203670	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203674	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727682	0.92[AMR][1000 genomes];0.97[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
rs12464878	CPS1	cis	Artery Tibial	GTEx
rs12464878	CPS1	cis	lung	GTEx
rs12464878	CPS1	cis	Adipose Subcutaneous	GTEx
rs12464878	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211340200-211343000	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:211340200-211343000	Active TSS	HSMMtube	muscle
3	chr2:211340200-211343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:211340400-211343000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:211340400-211343000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:211340400-211343000	Active TSS	Right Atrium	heart
7	chr2:211340400-211343000	Active TSS	GM12878-XiMat	blood
8	chr2:211340400-211343000	Active TSS	HSMM	muscle
9	chr2:211340400-211343200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:211340400-211343200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:211340400-211343200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:211340400-211343200	Active TSS	Ovary	ovary
13	chr2:211340400-211343200	Active TSS	NHLF	lung
14	chr2:211340400-211343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:211340600-211343000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:211340600-211343200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:211340600-211343200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:211340600-211343400	Active TSS	K562	blood
19	chr2:211340800-211343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:211340800-211343000	Active TSS	NH-A	brain
21	chr2:211340800-211343200	Active TSS	HMEC	breast
22	chr2:211340800-211343400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:211340800-211343400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:211340800-211343600	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:211341000-211343000	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:211341200-211343000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:211341400-211343000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:211341600-211343200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:211341600-211344800	Weak transcription	Spleen	Spleen
30	chr2:211341600-211347800	Weak transcription	Gastric	stomach
31	chr2:211341600-211348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:211341600-211348800	Weak transcription	Pancreas	Pancrea
33	chr2:211341800-211343000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr2:211341800-211343200	Flanking Active TSS	Dnd41	blood
35	chr2:211341800-211345000	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:211342000-211343000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:211342000-211343000	Enhancers	Brain Substantia Nigra	brain
38	chr2:211342000-211343800	Weak transcription	Small Intestine	intestine
39	chr2:211342200-211343000	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr2:211342200-211344800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:211342400-211343000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:211342400-211343000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:211342400-211343000	Active TSS	Rectal Smooth Muscle	rectum
44	chr2:211342400-211343200	Enhancers	Primary T cells from cord blood	blood
45	chr2:211342400-211343400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:211342400-211344800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:211342400-211346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:211342600-211343000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:211342600-211343000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:211342600-211343000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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