Variant report

Variant	rs359549
Chromosome Location	chr3:155271825-155271826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155268061..155270293-chr3:155271366..155273001,2	K562	blood:

Extended variants
information (count: 129 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10212586	0.82[ASN][1000 genomes]
rs10212592	0.83[ASN][1000 genomes]
rs10212593	0.83[ASN][1000 genomes]
rs10804772	0.84[ASN][1000 genomes]
rs10936006	0.90[JPT][hapmap]
rs10936012	0.84[ASN][1000 genomes]
rs10936014	0.86[JPT][hapmap];0.83[LWK][hapmap]
rs11707218	0.84[ASN][1000 genomes]
rs11924789	0.84[ASN][1000 genomes]
rs12485814	0.84[ASN][1000 genomes]
rs12632699	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12638084	0.85[ASN][1000 genomes]
rs13085349	0.84[ASN][1000 genomes]
rs13085986	0.84[ASN][1000 genomes]
rs1401695	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1589237	0.84[ASN][1000 genomes]
rs1607589	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607590	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1607591	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs173369	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs181696	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs183088	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs1878859	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1879089	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs189639	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1914799	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs1967426	0.81[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap]
rs2007826	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2015945	0.91[JPT][hapmap]
rs2102897	0.86[JPT][hapmap]
rs2203885	0.87[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs2315589	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs34936050	0.84[ASN][1000 genomes]
rs358726	0.81[JPT][hapmap]
rs358908	0.91[JPT][hapmap]
rs358909	0.91[JPT][hapmap]
rs359538	0.97[ASN][1000 genomes]
rs359539	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs359540	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs359542	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs359547	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs359548	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs359550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs359551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs359552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs359553	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs359554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs359555	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs359556	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs359557	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs359561	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs359562	0.87[ASN][1000 genomes]
rs359563	0.82[ASN][1000 genomes]
rs359564	0.87[ASN][1000 genomes]
rs359565	0.87[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs359566	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs359568	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs359569	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs359570	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs359572	0.92[ASN][1000 genomes]
rs359573	0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3908138	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3908139	0.84[ASN][1000 genomes]
rs3908140	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3908141	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs3908142	0.84[ASN][1000 genomes]
rs3908143	0.84[ASN][1000 genomes]
rs3908144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3914780	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4083042	0.87[ASN][1000 genomes]
rs4125975	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4287944	0.95[JPT][hapmap];0.93[YRI][hapmap]
rs4401403	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4680201	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680205	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.88[ASN][1000 genomes]
rs4680208	0.82[ASN][1000 genomes]
rs4680210	0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs484663	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486714	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs497397	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs500051	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517971	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs521073	0.87[ASN][1000 genomes]
rs531139	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs536008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538440	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs539240	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56229209	0.82[ASN][1000 genomes]
rs569813	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59567840	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62287281	0.84[ASN][1000 genomes]
rs628026	0.88[ASN][1000 genomes]
rs6440997	0.86[JPT][hapmap]
rs6440998	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6441002	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6441003	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs6441005	0.87[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs658283	0.88[ASN][1000 genomes]
rs673001	0.84[ASN][1000 genomes]
rs6767886	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs6768777	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6769807	0.86[JPT][hapmap]
rs6779500	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6787055	0.85[ASN][1000 genomes]
rs6793225	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6800331	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802475	0.84[ASN][1000 genomes]
rs7426747	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7433135	0.84[ASN][1000 genomes]
rs7609669	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7610604	0.83[ASN][1000 genomes]
rs7620630	0.82[ASN][1000 genomes]
rs7629025	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs7629557	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7641141	0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs783550	0.88[ASN][1000 genomes]
rs9809924	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs9814374	0.82[ASN][1000 genomes]
rs9814666	0.82[ASN][1000 genomes]
rs9818926	0.95[CEU][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9828161	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9828965	0.86[ASN][1000 genomes]
rs9844708	0.88[ASN][1000 genomes]
rs9844732	0.82[ASN][1000 genomes]
rs9845615	0.85[ASN][1000 genomes]
rs9865998	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9874559	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs359549	PLCH1	cis	cerebellum	SCAN
rs359549	SLC33A1	cis	cerebellum	SCAN
rs359549	SLC33A1	cis	parietal	SCAN
rs359549	PLCL3	cis	multi-tissue	Pritchard
rs359549	MLF1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155232200-155274000	Weak transcription	Pancreas	Pancrea
2	chr3:155241800-155273000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:155253600-155273600	Weak transcription	Gastric	stomach
4	chr3:155257000-155289600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:155259400-155284800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:155259400-155289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:155259800-155278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:155260000-155278200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:155260200-155302600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:155264200-155272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:155264400-155282200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:155265800-155273000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:155266000-155277800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:155266200-155287200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:155266800-155272200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:155266800-155274400	Weak transcription	Lung	lung
17	chr3:155267800-155278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:155267800-155278000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:155268000-155279800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:155268800-155272200	Weak transcription	Fetal Kidney	kidney
21	chr3:155268800-155272800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:155270200-155272000	Strong transcription	Fetal Intestine Large	intestine
23	chr3:155270200-155272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:155270400-155274600	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:155270400-155276800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:155270600-155278600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:155271200-155272000	Genic enhancers	A549	lung
28	chr3:155271200-155273000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:155271400-155272000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:155271400-155272200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:155271400-155272200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:155271400-155272200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:155271400-155272200	Flanking Active TSS	Fetal Thymus	thymus
34	chr3:155271400-155272200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr3:155271400-155273200	Enhancers	Primary B cells from cord blood	blood
36	chr3:155271400-155273200	Enhancers	Primary T cells from cord blood	blood
37	chr3:155271400-155273800	Enhancers	HMEC	breast
38	chr3:155271600-155272000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr3:155271600-155272000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:155271600-155272000	Strong transcription	Fetal Intestine Small	intestine
41	chr3:155271600-155272000	Enhancers	NHEK	skin
42	chr3:155271600-155273600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:155271600-155273800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:155271600-155273800	Flanking Active TSS	Dnd41	blood
45	chr3:155271800-155272000	Enhancers	Primary B cells from peripheral blood	blood
46	chr3:155271800-155272000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:155271800-155272200	Flanking Active TSS	Thymus	Thymus
48	chr3:155271800-155272200	Enhancers	GM12878-XiMat	blood
49	chr3:155271800-155273000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:155271800-155274200	Enhancers	HepG2	liver

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