Variant report

Variant	rs805404
Chromosome Location	chr2:54116800-54116801
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10183655	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs11683741	0.81[AMR][1000 genomes]
rs11689025	0.81[AMR][1000 genomes]
rs11890838	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs11898855	0.83[AMR][1000 genomes]
rs1232	0.87[CEU][hapmap]
rs17045199	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs17045452	0.91[CHB][hapmap];0.90[MEX][hapmap]
rs17045474	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs17045488	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2253760	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2302879	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542571	0.91[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap]
rs2542575	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2692514	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2692516	0.95[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs2692534	0.80[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs28851028	0.85[AMR][1000 genomes]
rs2909459	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes]
rs2949810	0.83[AMR][1000 genomes]
rs2949814	0.81[AMR][1000 genomes]
rs34498089	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs3731967	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs4671746	0.90[AMR][1000 genomes]
rs55692047	0.90[AMR][1000 genomes]
rs56302494	0.90[AMR][1000 genomes]
rs62139336	0.91[AMR][1000 genomes]
rs6545377	0.81[AMR][1000 genomes]
rs6545381	0.85[AMR][1000 genomes]
rs6714450	0.83[AMR][1000 genomes]
rs6746965	0.83[CHB][hapmap]
rs698855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698857	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7559384	0.82[AMR][1000 genomes]
rs7583622	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs766075	0.86[CHB][hapmap]
rs805310	0.91[CHB][hapmap];0.83[AMR][1000 genomes]
rs805311	0.81[AMR][1000 genomes]
rs805312	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805313	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805314	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805315	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805316	0.91[ASW][hapmap];0.91[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs805319	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805323	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805325	0.83[AMR][1000 genomes]
rs805326	0.83[AMR][1000 genomes]
rs805327	0.83[AMR][1000 genomes]
rs805328	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805329	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805337	0.82[AMR][1000 genomes]
rs805338	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs805340	0.81[AMR][1000 genomes]
rs805344	0.83[AMR][1000 genomes]
rs805346	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805347	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805348	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805349	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805354	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805355	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805356	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805357	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805362	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805363	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805376	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805377	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805378	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805382	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805384	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805385	0.82[AMR][1000 genomes]
rs805386	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805387	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805388	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805390	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805394	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805398	0.83[AMR][1000 genomes]
rs805399	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805400	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805401	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805406	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805407	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805408	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805409	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805411	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805413	0.83[AMR][1000 genomes]
rs805414	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805415	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805416	0.95[ASN][1000 genomes]
rs805419	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805420	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805425	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805426	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805428	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805429	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805446	0.87[CEU][hapmap]
rs805447	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs805449	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs805451	0.82[AMR][1000 genomes]
rs809281	0.81[AMR][1000 genomes]
rs809282	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs805404	PSME4	cis	lymphoblastoid	seeQTL
rs805404	PSME4	cis	cerebellum	SCAN
rs805404	ACYP2	cis	multi-tissue	Pritchard
rs805404	PRDXDD1P	cis	parietal	SCAN
rs805404	MTIF2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54087000-54168000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:54087400-54117400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54087400-54137600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54087600-54117000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
7	chr2:54088400-54137200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:54088600-54138000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:54089800-54136000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:54090200-54137800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:54090200-54138200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:54090400-54137600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:54090800-54137400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:54091000-54137000	Strong transcription	Fetal Thymus	thymus
15	chr2:54091000-54137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:54091000-54138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:54091200-54138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:54091400-54137600	Strong transcription	Liver	Liver
19	chr2:54093800-54124000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:54094000-54137800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:54099200-54137400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:54100400-54137800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:54100400-54137800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:54100400-54140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:54100600-54123000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr2:54100600-54137400	Strong transcription	Placenta	Placenta
27	chr2:54100600-54137800	Strong transcription	Primary B cells from cord blood	blood
28	chr2:54100600-54141200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:54100800-54138000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:54102000-54124400	Weak transcription	Small Intestine	intestine
31	chr2:54102200-54117400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:54103800-54129200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:54104600-54135600	Strong transcription	Primary T cells from cord blood	blood
34	chr2:54105800-54120400	Strong transcription	Fetal Intestine Large	intestine
35	chr2:54105800-54137200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:54106000-54120400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54106000-54138000	Strong transcription	Dnd41	blood
38	chr2:54106200-54138400	Strong transcription	Adipose Nuclei	Adipose
39	chr2:54106600-54137800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:54107000-54123800	Strong transcription	HMEC	breast
41	chr2:54107200-54123000	Strong transcription	K562	blood
42	chr2:54107200-54123200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:54107200-54124200	Strong transcription	HepG2	liver
44	chr2:54108200-54120400	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:54108200-54137400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:54108200-54177400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:54108400-54135600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:54108400-54137400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:54108600-54119600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:54108600-54135800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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