Variant report

Variant	rs4955412
Chromosome Location	chr3:49418168-49418169
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1050088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1050450	0.94[ASN][1000 genomes]
rs10640	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10865955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130192	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130194	0.89[EUR][1000 genomes]
rs11130196	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11130202	1.00[CEU][hapmap]
rs11706370	1.00[JPT][hapmap]
rs11711485	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11711536	0.94[ASN][1000 genomes]
rs11715915	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11716974	0.82[ASN][1000 genomes]
rs11720264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11922013	1.00[JPT][hapmap]
rs12489092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs13078949	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs13086611	0.94[ASN][1000 genomes]
rs13087851	0.94[ASN][1000 genomes]
rs13090388	0.94[ASN][1000 genomes]
rs13096760	0.91[EUR][1000 genomes]
rs1464566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs1568662	0.82[EUR][1000 genomes]
rs17080528	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17595772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650792	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800668	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1801143	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1987628	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2117939	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878298	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34588335	0.94[ASN][1000 genomes]
rs34937635	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35169793	0.94[ASN][1000 genomes]
rs35701831	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs3811697	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3811699	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3870337	0.80[EUR][1000 genomes]
rs3870338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs3877784	0.83[EUR][1000 genomes]
rs3924462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs3924463	0.81[EUR][1000 genomes]
rs4459909	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4563439	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4625	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs4855842	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855843	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs4855861	0.82[EUR][1000 genomes]
rs4855864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4855866	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955438	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957735	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59152804	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259942	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62261185	0.80[EUR][1000 genomes]
rs6446264	0.94[ASN][1000 genomes]
rs6446272	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6446274	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67485053	0.88[ASN][1000 genomes]
rs6766131	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6773518	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6779524	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6784820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793308	0.94[ASN][1000 genomes]
rs6797765	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809216	0.94[ASN][1000 genomes]
rs6997	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7371895	0.82[EUR][1000 genomes]
rs7373849	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621003	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622302	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7623659	0.94[ASN][1000 genomes]
rs7631908	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633271	1.00[JPT][hapmap]
rs7637999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs7643586	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643845	0.83[EUR][1000 genomes]
rs7645445	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7646366	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7648841	0.94[ASN][1000 genomes]
rs885592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9814873	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9827021	1.00[JPT][hapmap]
rs9837027	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9841110	1.00[JPT][hapmap]
rs9853683	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9858280	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4955412	P4HTM	cis	cerebellum	SCAN
rs4955412	WDR6	cis	lung	GTEx
rs4955412	IP6K2	cis	cerebellum	SCAN
rs4955412	QRICH1	cis	parietal	SCAN
rs4955412	WDR6	cis	parietal	SCAN
rs4955412	WDR6	cis	Muscle Skeletal	GTEx
rs4955412	WDR6	cis	Artery Tibial	GTEx
rs4955412	WDR6	cis	Nerve Tibial	GTEx
rs4955412	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4955412	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4955412	GNL3	cis	cerebellum	SCAN
rs4955412	CCDC71	cis	cerebellum	SCAN
rs4955412	P4HTM	cis	parietal	SCAN
rs4955412	DALRD3	cis	cerebellum	SCAN
rs4955412	WDR6	cis	Adipose Subcutaneous	GTEx
rs4955412	WDR6	cis	Whole Blood	GTEx
rs4955412	AMT	cis	cerebellum	SCAN
rs4955412	AMT	cis	Thyroid	GTEx
rs4955412	WDR6	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart
4	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:49410600-49421800	Weak transcription	K562	blood
7	chr3:49411000-49434600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:49411200-49418800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:49411200-49423200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:49411200-49423800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:49413000-49418800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:49413000-49421600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:49413000-49422000	Weak transcription	Pancreas	Pancrea
14	chr3:49413000-49423200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:49413000-49423800	Weak transcription	HUVEC	blood vessel
16	chr3:49413200-49419800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:49413200-49423200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:49413200-49423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:49413200-49423200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:49413200-49425400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:49413200-49425600	Weak transcription	Hela-S3	cervix
22	chr3:49413200-49431800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:49413200-49432000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:49413200-49432000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:49413200-49432000	Weak transcription	Fetal Kidney	kidney
26	chr3:49413200-49433200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:49413200-49435000	Weak transcription	Brain Angular Gyrus	brain
28	chr3:49413200-49441400	Weak transcription	Aorta	Aorta
29	chr3:49413200-49443000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:49413400-49423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:49413400-49425400	Weak transcription	Thymus	Thymus
33	chr3:49413400-49425400	Weak transcription	Dnd41	blood
34	chr3:49413400-49425600	Weak transcription	Fetal Intestine Large	intestine
35	chr3:49413400-49431800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:49413400-49433600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:49413400-49439000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:49413600-49418400	Weak transcription	HepG2	liver
39	chr3:49413600-49418600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:49413600-49418800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:49413600-49430600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:49413600-49432000	Weak transcription	Fetal Lung	lung
43	chr3:49413600-49433200	Weak transcription	Colonic Mucosa	Colon
44	chr3:49413600-49441000	Weak transcription	Fetal Brain Female	brain
45	chr3:49413800-49425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:49414400-49423200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:49414600-49419000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:49414600-49421400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:49414600-49424400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:49414600-49424400	Enhancers	Primary T helper cells PMA-I stimulated	--

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