Variant report

Variant	rs805338
Chromosome Location	chr2:54186536-54186537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54184085..54186543-chr2:54292825..54294983,2	K562	blood:
2	chr2:54185625..54188123-chr2:54194333..54197670,3	MCF-7	breast:
3	chr2:54184186..54188575-chr2:54196120..54198955,4	MCF-7	breast:
4	chr2:54182588..54184122-chr2:54186046..54188371,2	K562	blood:
5	chr2:54184275..54188127-chr2:54193177..54197889,6	K562	blood:
6	chr2:54179906..54182578-chr2:54184932..54187194,2	K562	blood:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1232	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][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]
rs2542582	0.92[CHB][hapmap]
rs2542589	0.93[CHB][hapmap]
rs2542591	0.93[CHB][hapmap]
rs2542592	1.00[CHB][hapmap]
rs2543629	0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2692519	0.92[CHB][hapmap]
rs2692533	0.92[CHB][hapmap]
rs2909459	0.81[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2949810	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2949813	0.92[CHB][hapmap]
rs2949814	0.92[AMR][1000 genomes]
rs34498089	1.00[YRI][hapmap]
rs4671746	0.80[AMR][1000 genomes]
rs55692047	0.80[AMR][1000 genomes]
rs56302494	0.80[AMR][1000 genomes]
rs62139336	0.82[AMR][1000 genomes]
rs6721970	0.92[YRI][hapmap]
rs698855	0.87[CEU][hapmap]
rs698857	0.80[AMR][1000 genomes]
rs805311	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs805313	0.82[AMR][1000 genomes]
rs805316	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs805321	0.83[CEU][hapmap]
rs805325	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805326	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805327	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs805337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805340	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805351	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs805352	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs805354	0.83[AMR][1000 genomes]
rs805355	0.83[AMR][1000 genomes]
rs805356	0.83[AMR][1000 genomes]
rs805357	0.83[AMR][1000 genomes]
rs805362	0.83[AMR][1000 genomes]
rs805365	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs805368	0.89[AMR][1000 genomes]
rs805383	0.91[AMR][1000 genomes]
rs805385	0.94[AMR][1000 genomes]
rs805397	0.82[AMR][1000 genomes]
rs805398	0.95[AMR][1000 genomes]
rs805399	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs805400	0.81[AMR][1000 genomes]
rs805401	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs805404	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs805406	0.80[AMR][1000 genomes]
rs805407	0.80[AMR][1000 genomes]
rs805408	0.80[AMR][1000 genomes]
rs805411	0.80[AMR][1000 genomes]
rs805413	0.95[AMR][1000 genomes]
rs805414	0.80[AMR][1000 genomes]
rs805426	0.82[CEU][hapmap]
rs805437	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs805446	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]
rs805447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805448	0.91[ASN][1000 genomes]
rs805449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805452	0.97[ASN][1000 genomes]
rs809281	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs809282	0.81[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs805338	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54151000-54189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:54153400-54194600	Weak transcription	Fetal Brain Male	brain
4	chr2:54156600-54188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54156600-54190000	Weak transcription	Spleen	Spleen
6	chr2:54159200-54188000	Weak transcription	Colonic Mucosa	Colon
7	chr2:54159200-54188000	Weak transcription	Esophagus	oesophagus
8	chr2:54159200-54188200	Weak transcription	Small Intestine	intestine
9	chr2:54159200-54189400	Weak transcription	Aorta	Aorta
10	chr2:54159200-54189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:54161600-54189800	Weak transcription	Ovary	ovary
13	chr2:54171000-54188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:54173400-54191400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:54174200-54195600	Weak transcription	Thymus	Thymus
16	chr2:54174400-54188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:54174400-54188600	Weak transcription	GM12878-XiMat	blood
18	chr2:54175200-54193000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:54175200-54195400	Weak transcription	Fetal Stomach	stomach
20	chr2:54175400-54188400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:54175800-54189800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:54175800-54190000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:54176000-54187800	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:54176000-54189800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:54176200-54188400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:54176200-54188400	Weak transcription	HMEC	breast
27	chr2:54176200-54188600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:54176200-54189800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:54176200-54189800	Weak transcription	NH-A	brain
30	chr2:54176200-54191600	Weak transcription	NHDF-Ad	bronchial
31	chr2:54176200-54192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:54176200-54194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54176200-54194600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:54176200-54195400	Weak transcription	Fetal Intestine Large	intestine
35	chr2:54176200-54195400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:54176200-54196000	Weak transcription	Fetal Thymus	thymus
37	chr2:54176200-54196200	Weak transcription	Placenta	Placenta
38	chr2:54176400-54187800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:54176400-54188200	Weak transcription	Primary T cells from cord blood	blood
40	chr2:54176400-54188400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:54176400-54189000	Weak transcription	Fetal Kidney	kidney
42	chr2:54176400-54194800	Weak transcription	NHLF	lung
43	chr2:54176400-54195000	Weak transcription	HSMM	muscle
44	chr2:54176600-54188600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr2:54176600-54189200	Weak transcription	Adipose Nuclei	Adipose
46	chr2:54176800-54188400	Weak transcription	NHEK	skin
47	chr2:54176800-54192200	Weak transcription	Hela-S3	cervix
48	chr2:54177000-54188000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:54177000-54189800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:54177000-54189800	Weak transcription	Dnd41	blood

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