Variant report

Variant	rs1232
Chromosome Location	chr2:54082405-54082406
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54080524..54082859-chr2:54093710..54096577,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs11897282	0.84[CHB][hapmap]
rs11901698	0.84[CHB][hapmap]
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];0.83[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];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][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];0.89[MEX][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];0.84[MEX][hapmap]
rs2949810	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2949813	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2949814	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770394	0.84[CHB][hapmap]
rs3770397	0.80[ASN][1000 genomes]
rs4116709	0.92[CHB][hapmap]
rs62137602	0.80[ASN][1000 genomes]
rs698855	0.87[CEU][hapmap]
rs719127	0.84[CHB][hapmap]
rs805311	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805316	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805321	0.87[CEU][hapmap]
rs805325	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805326	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805327	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805328	0.81[CEU][hapmap]
rs805334	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs805337	0.88[AMR][1000 genomes]
rs805338	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes]
rs805340	0.86[AMR][1000 genomes]
rs805351	0.87[CEU][hapmap]
rs805352	0.87[CEU][hapmap]
rs805365	0.87[CEU][hapmap]
rs805368	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805383	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805385	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805386	0.87[CEU][hapmap]
rs805398	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805399	0.91[CEU][hapmap]
rs805401	0.83[CEU][hapmap]
rs805404	0.87[CEU][hapmap]
rs805408	0.87[CEU][hapmap]
rs805413	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805426	0.91[CEU][hapmap]
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];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805447	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805449	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805451	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs809281	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1232	RAE1	trans	cerebellum	SCAN
rs1232	PSME4	cis	cerebellum	SCAN
rs1232	MTIF2	cis	cerebellum	SCAN
rs1232	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs1232	PSME4	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54074800-54096600	Weak transcription	Hela-S3	cervix
3	chr2:54075000-54084000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:54076400-54082600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54077000-54085800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54078600-54086800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:54078600-54092200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:54078800-54092400	Weak transcription	K562	blood
9	chr2:54079000-54091800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:54079200-54086800	Weak transcription	Colonic Mucosa	Colon
11	chr2:54079400-54086200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:54079600-54086400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:54079600-54090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:54079800-54083400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:54080000-54083600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:54080000-54083800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:54080000-54083800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:54080000-54083800	Strong transcription	Dnd41	blood
19	chr2:54080200-54082600	Strong transcription	NHDF-Ad	bronchial
20	chr2:54080200-54082800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:54080200-54082800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr2:54080200-54082800	Strong transcription	Spleen	Spleen
23	chr2:54080200-54083400	Strong transcription	Primary T cells from cord blood	blood
24	chr2:54080200-54083800	Strong transcription	Primary B cells from cord blood	blood
25	chr2:54080200-54086800	Weak transcription	Right Atrium	heart
26	chr2:54080400-54083000	Strong transcription	Adipose Nuclei	Adipose
27	chr2:54080400-54086000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:54080600-54083600	Strong transcription	Fetal Thymus	thymus
29	chr2:54080600-54083800	Strong transcription	NHEK	skin
30	chr2:54081200-54091800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:54081600-54086200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:54081600-54086800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:54081600-54087000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:54081600-54090600	Weak transcription	HUVEC	blood vessel
35	chr2:54081600-54091200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:54081600-54091600	Weak transcription	HSMMtube	muscle
37	chr2:54081800-54082600	Weak transcription	Brain Angular Gyrus	brain
38	chr2:54081800-54082800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:54081800-54085400	Weak transcription	Liver	Liver
40	chr2:54081800-54085600	Weak transcription	Fetal Brain Female	brain
41	chr2:54081800-54086200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:54081800-54086400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:54081800-54086400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:54081800-54086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54081800-54086400	Weak transcription	Esophagus	oesophagus
46	chr2:54081800-54086400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:54081800-54086800	Weak transcription	Gastric	stomach
48	chr2:54081800-54086800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:54081800-54086800	Weak transcription	Right Ventricle	heart
50	chr2:54081800-54087000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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