Variant report

Variant	rs62203672
Chromosome Location	chr2:211343357-211343358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs12464878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1396954	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17552879	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042049	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287418	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287419	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287420	0.97[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	0.94[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	0.97[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	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856348	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856349	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672575	0.91[ASN][1000 genomes]
rs4672577	0.89[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	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4673532	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4673533	0.84[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]
rs62203673	0.97[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	0.89[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
rs62203672	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs62203672	CPS1	cis	lung	GTEx
rs62203672	CPS1	cis	Adipose Subcutaneous	GTEx
rs62203672	CPS1	cis	Artery Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211340400-211343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:211340600-211343400	Active TSS	K562	blood
3	chr2:211340800-211343400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:211340800-211343400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:211340800-211343600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:211341600-211344800	Weak transcription	Spleen	Spleen
7	chr2:211341600-211347800	Weak transcription	Gastric	stomach
8	chr2:211341600-211348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:211341600-211348800	Weak transcription	Pancreas	Pancrea
10	chr2:211341800-211345000	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:211342000-211343800	Weak transcription	Small Intestine	intestine
12	chr2:211342200-211344800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:211342400-211343400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:211342400-211344800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:211342400-211346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:211342600-211344000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:211342600-211344800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:211342600-211344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:211342600-211346200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:211342600-211348000	Weak transcription	Fetal Intestine Small	intestine
21	chr2:211342800-211343400	Flanking Active TSS	HepG2	liver
22	chr2:211342800-211343400	Flanking Active TSS	NHEK	skin
23	chr2:211342800-211344000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:211342800-211346200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:211342800-211346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:211343000-211343400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:211343000-211343400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:211343000-211343600	Weak transcription	HSMM	muscle
29	chr2:211343000-211344800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:211343000-211344800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:211343000-211345800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:211343000-211346000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:211343000-211346200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:211343000-211355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:211343200-211343400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:211343200-211343400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:211343200-211343400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr2:211343200-211343400	Enhancers	Dnd41	blood
39	chr2:211343200-211343400	Active TSS	NHDF-Ad	bronchial
40	chr2:211343200-211344800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:211343200-211344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:211343200-211344800	Weak transcription	HMEC	breast
43	chr2:211343200-211345800	Weak transcription	Hela-S3	cervix
44	chr2:211343200-211346200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:211343200-211348000	Weak transcription	Ovary	ovary

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