Variant report

Variant	rs2302879
Chromosome Location	chr2:54152927-54152928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54146828..54149502-chr2:54150581..54153087,2	K562	blood:
2	chr2:54151314..54153271-chr2:54161912..54164849,2	K562	blood:
3	chr2:54151686..54155492-chr2:54156781..54159253,3	K562	blood:
4	chr2:54149553..54153900-chr2:54153925..54156582,5	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10183655	0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs11683741	0.81[AMR][1000 genomes]
rs11689025	0.81[AMR][1000 genomes]
rs11890838	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs11898855	0.81[AMR][1000 genomes]
rs1232	0.87[CEU][hapmap]
rs17039547	0.82[ASW][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs17045199	0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs17045452	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs17045474	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs17045488	0.87[CHB][hapmap]
rs2253760	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2287643	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2542571	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2542575	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2692514	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2692516	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs2692534	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs28851028	0.82[AMR][1000 genomes]
rs2909459	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes]
rs2949810	0.84[AMR][1000 genomes]
rs2949815	0.82[AMR][1000 genomes]
rs34498089	0.81[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap]
rs3731967	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4671746	0.90[AMR][1000 genomes]
rs55692047	0.87[AMR][1000 genomes]
rs56302494	0.90[AMR][1000 genomes]
rs62139336	0.89[AMR][1000 genomes]
rs6545377	0.81[AMR][1000 genomes]
rs6545381	0.82[AMR][1000 genomes]
rs6713088	0.89[JPT][hapmap]
rs6714450	0.81[AMR][1000 genomes]
rs6721970	0.80[ASW][hapmap]
rs6746965	0.83[CHB][hapmap]
rs698855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs698857	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7559384	0.82[AMR][1000 genomes]
rs805310	0.91[CHB][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs805312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805313	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805314	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805315	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805316	0.91[ASW][hapmap];0.91[CEU][hapmap];0.85[MEX][hapmap]
rs805319	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805325	0.84[AMR][1000 genomes]
rs805326	0.84[AMR][1000 genomes]
rs805327	0.84[AMR][1000 genomes]
rs805328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805329	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805334	0.81[YRI][hapmap]
rs805338	0.87[CEU][hapmap]
rs805344	0.83[AMR][1000 genomes]
rs805346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805347	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805348	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805349	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs805354	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805355	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805356	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs805357	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs805360	0.83[YRI][hapmap]
rs805362	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805363	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805376	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs805377	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs805378	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs805382	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs805384	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805386	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805387	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805388	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805390	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805394	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805397	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805398	0.81[AMR][1000 genomes]
rs805399	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805400	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805401	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.94[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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805406	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805407	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805408	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805409	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805411	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805413	0.81[AMR][1000 genomes]
rs805414	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805415	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805416	0.85[ASN][1000 genomes]
rs805419	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805420	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805425	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805426	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805428	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805429	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805446	0.87[CEU][hapmap]
rs805447	0.87[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs805449	0.87[CEU][hapmap]
rs809281	0.81[AMR][1000 genomes]
rs809282	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2302879	RPS6KA5	trans	parietal	SCAN
rs2302879	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs2302879	PSME4	cis	cerebellum	SCAN
rs2302879	MTIF2	cis	cerebellum	SCAN
rs2302879	PSME4	cis	lymphoblastoid	seeQTL
rs2302879	PSME4	cis	multi-tissue	Pritchard
rs2302879	RAE1	trans	cerebellum	SCAN

Chromatin state (count:126 , 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	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
4	chr2:54108200-54177400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:54109800-54179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:54122200-54172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54124400-54159200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:54126200-54167600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:54127000-54156000	Weak transcription	Pancreas	Pancrea
10	chr2:54129000-54157600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:54133000-54153000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:54133000-54157800	Weak transcription	Colonic Mucosa	Colon
13	chr2:54133200-54154800	Weak transcription	Aorta	Aorta
14	chr2:54133400-54154800	Weak transcription	Spleen	Spleen
15	chr2:54135600-54172200	Weak transcription	Fetal Heart	heart
16	chr2:54139200-54176600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:54139200-54177000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:54139400-54153600	Weak transcription	Gastric	stomach
19	chr2:54139400-54158400	Strong transcription	A549	lung
20	chr2:54139400-54167200	Strong transcription	Liver	Liver
21	chr2:54139400-54167800	Strong transcription	Dnd41	blood
22	chr2:54139400-54176200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:54139600-54170800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:54139600-54177000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:54141200-54161400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:54141200-54166200	Strong transcription	Primary B cells from cord blood	blood
27	chr2:54141200-54167200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:54141400-54166600	Strong transcription	NH-A	brain
29	chr2:54141400-54167400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:54141400-54167600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:54141400-54170600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:54141600-54167000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:54141600-54167000	Strong transcription	Osteobl	bone
34	chr2:54142000-54165000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:54142000-54165600	Strong transcription	Adipose Nuclei	Adipose
36	chr2:54142000-54167200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:54142000-54167200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:54142200-54167200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:54142200-54167800	Strong transcription	HSMM	muscle
40	chr2:54142400-54166200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:54142400-54166600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:54142600-54153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:54143000-54166200	Strong transcription	HUVEC	blood vessel
44	chr2:54143000-54177600	Strong transcription	HepG2	liver
45	chr2:54143200-54167400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:54143400-54162200	Strong transcription	NHDF-Ad	bronchial
47	chr2:54143400-54165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:54143400-54167000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:54143400-54176200	Strong transcription	HMEC	breast
50	chr2:54144200-54166600	Strong transcription	Duodenum Mucosa	Duodenum

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