Variant report

Variant	rs359565
Chromosome Location	chr3:155308872-155308873
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10936006	0.80[JPT][hapmap]
rs10936014	0.85[JPT][hapmap]
rs12632699	0.90[JPT][hapmap]
rs1401695	0.90[JPT][hapmap]
rs1607589	0.83[ASN][1000 genomes]
rs1607590	0.90[JPT][hapmap]
rs1607591	0.91[JPT][hapmap]
rs173369	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs181696	0.85[JPT][hapmap]
rs183088	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap]
rs1878859	0.88[JPT][hapmap]
rs1879089	0.90[JPT][hapmap]
rs189639	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1914799	0.90[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs2007826	0.82[ASN][1000 genomes]
rs2015945	0.89[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs2102897	0.88[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2203885	0.85[JPT][hapmap]
rs2315589	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2315590	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs358726	0.82[JPT][hapmap]
rs358908	0.82[JPT][hapmap]
rs358909	0.82[JPT][hapmap]
rs359538	0.81[ASN][1000 genomes]
rs359539	0.87[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs359540	0.85[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs359542	0.85[JPT][hapmap]
rs359549	0.87[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs359551	0.91[JPT][hapmap]
rs359552	0.91[JPT][hapmap]
rs359553	0.90[JPT][hapmap]
rs359554	0.91[JPT][hapmap]
rs359555	0.82[ASN][1000 genomes]
rs359556	0.91[JPT][hapmap]
rs359557	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs359561	0.90[JPT][hapmap]
rs359566	0.90[JPT][hapmap]
rs359568	0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs359569	0.92[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs359570	0.92[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs359572	0.84[ASN][1000 genomes]
rs359573	0.83[ASN][1000 genomes]
rs3908138	0.90[JPT][hapmap]
rs3908140	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3908141	0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs3908144	0.95[JPT][hapmap]
rs3914780	0.90[JPT][hapmap]
rs407033	0.81[AMR][1000 genomes]
rs4125975	0.90[JPT][hapmap]
rs4287944	0.84[JPT][hapmap]
rs4401403	0.90[JPT][hapmap]
rs4680201	0.90[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs4680205	0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4680209	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4680210	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680211	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs484663	0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs486714	0.82[ASN][1000 genomes]
rs497397	0.82[ASN][1000 genomes]
rs500051	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs517971	0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs531139	0.84[ASN][1000 genomes]
rs536008	0.91[JPT][hapmap]
rs537730	0.81[ASN][1000 genomes]
rs538440	0.84[ASN][1000 genomes]
rs539240	0.80[ASN][1000 genomes]
rs569813	0.85[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs578492	0.90[JPT][hapmap]
rs6440997	0.85[JPT][hapmap]
rs6440998	0.85[JPT][hapmap]
rs6441002	0.91[JPT][hapmap]
rs6441003	0.91[JPT][hapmap]
rs6441005	0.85[JPT][hapmap]
rs6441009	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6767886	0.91[JPT][hapmap]
rs6768777	0.90[JPT][hapmap]
rs6769807	0.88[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6779500	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6793225	0.90[JPT][hapmap]
rs6800331	0.80[ASN][1000 genomes]
rs7609669	0.90[JPT][hapmap]
rs7620748	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629025	0.90[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs7629557	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7641141	0.91[JPT][hapmap]
rs9809924	0.89[JPT][hapmap]
rs9818926	0.95[JPT][hapmap]
rs9828161	0.91[JPT][hapmap]
rs9844708	0.81[ASN][1000 genomes]
rs9865998	0.91[JPT][hapmap]
rs9874559	0.90[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs359565	SLC33A1	cis	parietal	SCAN
rs359565	MLF1	cis	parietal	SCAN
rs359565	PLCH1	cis	cerebellum	SCAN
rs359565	SLC33A1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155273400-155312800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155275600-155311800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:155275600-155312800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:155283000-155315000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:155289600-155315000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:155290200-155322200	Weak transcription	A549	lung
7	chr3:155297800-155310600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:155303000-155313800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:155303600-155309200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:155303600-155310400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:155303600-155310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:155303600-155310600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:155303600-155324400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:155304000-155309000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:155304000-155310600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:155304000-155317000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:155304000-155325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:155308200-155322800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:155308400-155311800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:155308800-155312800	Weak transcription	Stomach Mucosa	stomach

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