Variant report

Variant	rs2222275
Chromosome Location	chr3:155358879-155358880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1005736	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1007920	0.87[ASN][1000 genomes]
rs10936011	0.82[ASN][1000 genomes]
rs10936013	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12486000	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12488043	0.87[ASN][1000 genomes]
rs12488087	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12490748	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12493067	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs13060809	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13076587	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077520	0.81[ASN][1000 genomes]
rs13079863	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082287	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13084995	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13087389	0.95[ASN][1000 genomes]
rs13089059	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095140	0.87[ASN][1000 genomes]
rs1519531	0.85[ASN][1000 genomes]
rs1519532	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1519533	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1519534	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1519535	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1568360	0.87[ASN][1000 genomes]
rs168601	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs173384	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1835212	0.81[JPT][hapmap]
rs1879090	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879091	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1879092	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2203886	0.90[ASN][1000 genomes]
rs34810038	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358704	0.86[JPT][hapmap]
rs358706	0.90[JPT][hapmap]
rs358707	0.90[JPT][hapmap]
rs358708	0.90[JPT][hapmap]
rs358727	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs358732	0.88[MEX][hapmap]
rs358742	0.84[MEX][hapmap]
rs358896	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358897	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358898	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358899	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358902	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358903	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs358904	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358905	0.93[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358906	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358910	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358911	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358912	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs359541	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs359543	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs359545	0.87[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs359546	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs359560	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs359567	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs386867	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4083041	0.80[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs412664	0.90[JPT][hapmap]
rs417877	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4618256	0.81[ASN][1000 genomes]
rs4679748	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs498378	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs592982	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs597718	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs60592119	0.88[ASN][1000 genomes]
rs629698	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs6441000	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6441006	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67428377	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6772682	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6777741	0.85[JPT][hapmap]
rs67955071	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6808257	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs687462	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7428196	0.86[JPT][hapmap]
rs7645831	0.85[JPT][hapmap]
rs9289956	0.81[JPT][hapmap]
rs934593	0.81[JPT][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	esv3450543	chr3:155356306-155360550	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2222275	PLCH1	cis	cerebellum	SCAN
rs2222275	SLC33A1	cis	parietal	SCAN
rs2222275	SLC33A1	cis	cerebellum	SCAN
rs2222275	SMC4	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155350400-155360000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:155352600-155359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:155354000-155363400	Weak transcription	Fetal Intestine Small	intestine
4	chr3:155355800-155363600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:155355800-155366600	Weak transcription	Pancreas	Pancrea
6	chr3:155357000-155359600	Weak transcription	Fetal Stomach	stomach
7	chr3:155357400-155360000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:155357400-155379000	Weak transcription	Gastric	stomach
9	chr3:155357800-155361800	Weak transcription	Stomach Mucosa	stomach
10	chr3:155358200-155359200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:155358200-155359800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:155358200-155359800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:155358200-155363600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:155358200-155364400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:155358200-155364600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:155358200-155364800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:155358200-155366000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:155358200-155366200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:155358400-155361400	Weak transcription	A549	lung
20	chr3:155358400-155363800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:155358400-155366000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:155358800-155363400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:155358800-155363600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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