Variant report

Variant	rs805446
Chromosome Location	chr2:54175905-54175906
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54174802..54180100-chr2:54196834..54199105,5	K562	blood:
2	chr2:54169107..54171499-chr2:54174293..54176041,2	MCF-7	breast:
3	chr2:54169796..54171728-chr2:54173892..54176111,2	K562	blood:
4	chr2:54174239..54176293-chr2:54179701..54182021,2	MCF-7	breast:
5	chr2:54173721..54175939-chr2:54181510..54183998,2	K562	blood:
6	chr2:54174064..54177025-chr2:54196606..54198334,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1232	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17039547	0.92[YRI][hapmap]
rs17045203	0.84[CHB][hapmap]
rs2287340	0.84[CHB][hapmap]
rs2287643	0.92[YRI][hapmap]
rs2542572	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2542582	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs2542589	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2542591	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2542592	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2543629	0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2692519	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2692533	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2909459	0.81[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2949810	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2949813	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs2949814	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34498089	1.00[YRI][hapmap]
rs6721970	0.92[YRI][hapmap]
rs698855	0.87[CEU][hapmap]
rs805311	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805316	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805321	0.83[CEU][hapmap]
rs805325	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805326	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805327	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805334	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs805337	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805340	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs805351	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs805352	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs805353	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs805354	0.81[AMR][1000 genomes]
rs805355	0.81[AMR][1000 genomes]
rs805356	0.81[AMR][1000 genomes]
rs805357	0.81[AMR][1000 genomes]
rs805362	0.81[AMR][1000 genomes]
rs805363	0.82[AMR][1000 genomes]
rs805365	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs805368	0.86[AMR][1000 genomes]
rs805383	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805385	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805398	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805399	0.82[CEU][hapmap]
rs805401	0.83[CEU][hapmap]
rs805404	0.87[CEU][hapmap]
rs805413	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805426	0.82[CEU][hapmap]
rs805437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs805447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805448	0.91[ASN][1000 genomes]
rs805449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805451	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805452	0.94[ASN][1000 genomes]
rs809281	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs805446	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	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
3	chr2:54108200-54177400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:54109800-54179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:54139200-54176600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54139200-54177000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:54139400-54176200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:54139600-54177000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:54143000-54177600	Strong transcription	HepG2	liver
10	chr2:54143400-54176200	Strong transcription	HMEC	breast
11	chr2:54149800-54177000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:54151000-54189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:54153200-54179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:54153400-54194600	Weak transcription	Fetal Brain Male	brain
15	chr2:54156600-54188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:54156600-54190000	Weak transcription	Spleen	Spleen
17	chr2:54159200-54177000	Weak transcription	Pancreas	Pancrea
18	chr2:54159200-54177200	Weak transcription	Right Ventricle	heart
19	chr2:54159200-54188000	Weak transcription	Colonic Mucosa	Colon
20	chr2:54159200-54188000	Weak transcription	Esophagus	oesophagus
21	chr2:54159200-54188200	Weak transcription	Small Intestine	intestine
22	chr2:54159200-54189400	Weak transcription	Aorta	Aorta
23	chr2:54159200-54189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54160800-54177200	Weak transcription	Lung	lung
26	chr2:54160800-54179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:54161600-54189800	Weak transcription	Ovary	ovary
28	chr2:54163600-54180400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:54164000-54176400	Weak transcription	Fetal Brain Female	brain
30	chr2:54164200-54177000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:54164800-54176600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:54167000-54176400	Weak transcription	NHEK	skin
33	chr2:54167600-54176400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:54169000-54177400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:54169200-54176400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:54170000-54176200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:54170000-54176800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:54171000-54188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54171800-54176200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:54172000-54176200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:54172000-54176200	Strong transcription	NH-A	brain
42	chr2:54172400-54176000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:54172400-54176000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:54172400-54176600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:54172400-54177000	Strong transcription	Dnd41	blood
46	chr2:54172600-54176200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:54172600-54176200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:54172600-54176200	Strong transcription	Fetal Thymus	thymus
49	chr2:54172600-54176400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:54172800-54176200	Strong transcription	Fetal Intestine Large	intestine

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