Variant report

Variant	rs805385
Chromosome Location	chr2:54097112-54097113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs11897282	0.84[CHB][hapmap]
rs11901698	0.84[CHB][hapmap]
rs1232	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408029	0.91[CHB][hapmap]
rs17045176	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs17045203	0.84[CHB][hapmap]
rs17520505	0.92[CHB][hapmap]
rs2287340	0.84[CHB][hapmap]
rs2302797	0.84[CHB][hapmap]
rs2542572	0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2542573	0.89[ASN][1000 genomes]
rs2542578	0.89[ASN][1000 genomes]
rs2542580	0.89[ASN][1000 genomes]
rs2542582	0.92[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs2542589	0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2542590	0.88[ASN][1000 genomes]
rs2542591	0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2542592	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2543629	0.80[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs2692512	0.92[ASN][1000 genomes]
rs2692513	0.92[ASN][1000 genomes]
rs2692519	0.92[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2692521	0.90[ASN][1000 genomes]
rs2692522	0.89[ASN][1000 genomes]
rs2692523	0.89[ASN][1000 genomes]
rs2692533	0.92[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs2909459	0.83[YRI][hapmap]
rs2949810	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2949813	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2949814	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770394	0.84[CHB][hapmap]
rs3770397	0.80[ASN][1000 genomes]
rs3770411	0.80[CHD][hapmap]
rs4116709	0.92[CHB][hapmap]
rs62137602	0.80[ASN][1000 genomes]
rs698855	0.92[ASW][hapmap];0.87[CEU][hapmap];0.86[MEX][hapmap]
rs698857	0.83[AMR][1000 genomes]
rs719127	0.84[CHB][hapmap]
rs805311	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs805313	0.82[AMR][1000 genomes]
rs805316	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805321	0.87[CEU][hapmap]
rs805325	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805326	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805327	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805328	0.81[CEU][hapmap]
rs805329	0.81[AMR][1000 genomes]
rs805334	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs805337	0.94[AMR][1000 genomes]
rs805338	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes]
rs805340	0.92[AMR][1000 genomes]
rs805351	0.87[CEU][hapmap]
rs805352	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs805353	0.82[AFR][1000 genomes]
rs805365	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs805368	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805383	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805384	0.80[AMR][1000 genomes]
rs805386	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs805387	0.80[AMR][1000 genomes]
rs805388	0.83[AMR][1000 genomes]
rs805390	0.83[AMR][1000 genomes]
rs805394	0.85[AMR][1000 genomes]
rs805397	0.82[AMR][1000 genomes]
rs805398	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805399	0.91[CEU][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs805400	0.83[AMR][1000 genomes]
rs805401	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs805404	0.87[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs805406	0.83[AMR][1000 genomes]
rs805407	0.83[AMR][1000 genomes]
rs805408	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs805409	0.85[AMR][1000 genomes]
rs805411	0.83[AMR][1000 genomes]
rs805413	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805414	0.83[AMR][1000 genomes]
rs805415	0.82[AMR][1000 genomes]
rs805419	0.82[AMR][1000 genomes]
rs805420	0.82[AMR][1000 genomes]
rs805425	0.81[AMR][1000 genomes]
rs805426	0.91[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs805435	0.89[ASN][1000 genomes]
rs805437	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs805446	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805447	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805449	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805451	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs809281	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs809282	0.83[AMR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs805385	MTIF2	cis	cerebellum	SCAN
rs805385	RAE1	trans	cerebellum	SCAN
rs805385	PSME4	cis	cerebellum	SCAN
rs805385	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54084000-54102000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:54085400-54106600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:54086600-54101200	Weak transcription	Fetal Brain Male	brain
4	chr2:54087000-54168000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:54087400-54097400	Strong transcription	Primary B cells from cord blood	blood
7	chr2:54087400-54112200	Weak transcription	Psoas Muscle	Psoas
8	chr2:54087400-54112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:54087400-54117400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:54087400-54137600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:54087600-54100800	Weak transcription	Brain Angular Gyrus	brain
12	chr2:54087600-54110800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:54087600-54113600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:54087600-54116600	Weak transcription	Pancreas	Pancrea
15	chr2:54087600-54117000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
17	chr2:54087800-54112200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:54088000-54113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:54088200-54100800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:54088400-54137200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:54088600-54138000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:54089200-54104400	Strong transcription	Osteobl	bone
23	chr2:54089800-54106200	Strong transcription	Left Ventricle	heart
24	chr2:54089800-54136000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:54090000-54098800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:54090200-54097600	Strong transcription	HSMM	muscle
27	chr2:54090200-54103600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:54090200-54107400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54090200-54137800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:54090200-54138200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:54090400-54098000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:54090400-54098600	Strong transcription	Primary T cells from cord blood	blood
33	chr2:54090400-54103800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:54090400-54137600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:54090800-54099600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:54090800-54137400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:54091000-54098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:54091000-54137000	Strong transcription	Fetal Thymus	thymus
39	chr2:54091000-54137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:54091000-54138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:54091200-54097200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr2:54091200-54097400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:54091200-54097800	Strong transcription	Adipose Nuclei	Adipose
44	chr2:54091200-54098200	Strong transcription	NH-A	brain
45	chr2:54091200-54098800	Strong transcription	Dnd41	blood
46	chr2:54091200-54138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:54091400-54137600	Strong transcription	Liver	Liver
48	chr2:54091800-54097200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr2:54091800-54104400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:54092000-54097200	Strong transcription	GM12878-XiMat	blood

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