Variant report

Variant	rs7554904
Chromosome Location	chr1:165510533-165510534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10737514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753683	0.90[ASN][1000 genomes]
rs10800108	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10918207	0.91[YRI][hapmap]
rs10918216	0.90[ASN][1000 genomes]
rs10918217	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10918218	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12025040	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12043239	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1326376	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1425754	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572541	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1572542	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2348725	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2433137	0.96[CEU][hapmap];0.87[MEX][hapmap]
rs6657863	0.92[JPT][hapmap]
rs722259	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7537189	0.82[YRI][hapmap]
rs7550844	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7554904	MGST3	cis	lymphoblastoid	seeQTL
rs7554904	ILDR2	cis	parietal	SCAN
rs7554904	MGST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165505600-165513000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:165507600-165512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:165508400-165510800	Enhancers	Fetal Muscle Leg	muscle
4	chr1:165508400-165510800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:165508600-165510600	Enhancers	Left Ventricle	heart
6	chr1:165509000-165510600	Enhancers	Psoas Muscle	Psoas
7	chr1:165509600-165510600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:165509600-165510600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:165509800-165511400	Weak transcription	Fetal Lung	lung
10	chr1:165509800-165511800	Weak transcription	Fetal Stomach	stomach
11	chr1:165510000-165510800	Enhancers	Fetal Heart	heart
12	chr1:165510200-165511000	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:165510200-165513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:165510400-165512400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:165510400-165512800	Weak transcription	Adipose Nuclei	Adipose
16	chr1:165510400-165512800	Weak transcription	Placenta	Placenta
17	chr1:165510400-165512800	Weak transcription	Right Atrium	heart
18	chr1:165510400-165512800	Weak transcription	Right Ventricle	heart
19	chr1:165510400-165513000	Weak transcription	Brain Inferior Temporal Lobe	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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