Variant report

Variant	rs3856348
Chromosome Location	chr2:211345996-211345997
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10932334	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10932339	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs12464878	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474078	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12618926	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12623942	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1396954	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1509820	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[YRI][hapmap]
rs17552879	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007748	0.89[CEU][hapmap];0.91[YRI][hapmap]
rs2042049	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287419	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2287422	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2370948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732055	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3770687	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770690	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770691	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856340	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3856343	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856344	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856345	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856346	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856347	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856349	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672575	0.90[ASN][1000 genomes]
rs4672577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4673530	0.97[ASN][1000 genomes]
rs4673531	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4673532	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4673533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203668	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203669	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203670	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203672	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203673	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203674	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727682	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569252	0.86[ASN][1000 genomes]
rs7580046	0.89[CEU][hapmap];0.91[YRI][hapmap]
rs7603241	0.89[CEU][hapmap];0.91[YRI][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3856348	LANCL1	cis	parietal	SCAN
rs3856348	CPS1	cis	lung	GTEx
rs3856348	CPS1	cis	Artery Tibial	GTEx
rs3856348	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs3856348	CPS1	cis	cerebellum	SCAN
rs3856348	CPS1	cis	Adipose Subcutaneous	GTEx
rs3856348	LANCL1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211341600-211347800	Weak transcription	Gastric	stomach
2	chr2:211341600-211348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:211341600-211348800	Weak transcription	Pancreas	Pancrea
4	chr2:211342400-211346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:211342600-211346200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:211342600-211348000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:211342800-211346200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:211342800-211346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:211343000-211346000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:211343000-211346200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:211343000-211355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:211343200-211346200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:211343200-211348000	Weak transcription	Ovary	ovary
14	chr2:211343400-211346600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:211343400-211347800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:211343400-211363600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:211343600-211346200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:211343800-211346400	Weak transcription	HSMM	muscle
19	chr2:211344000-211348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:211344000-211350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:211345200-211346200	Weak transcription	NHEK	skin
22	chr2:211345200-211346600	Weak transcription	HMEC	breast
23	chr2:211345400-211346600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:211345600-211346000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:211345600-211346600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:211345600-211349600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:211345800-211346200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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