Variant report

Variant	rs6426925
Chromosome Location	chr1:165598854-165598855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:165598443-165602604	K562	blood:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165599593-165599602 chr1:165601292-165601302 chr1:165601697-165601708 chr1:165599071-165599085
2	HCFC1	chr1:165598793-165601947	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:165598732..165600312-chr1:165601060..165603402,2	MCF-7	breast:
2	chr1:165598510..165600017-chr1:165872095..165874763,2	K562	blood:
3	chr1:165598675..165601057-chr1:165860826..165863471,2	K562	blood:
4	chr1:165597760..165600070-chr1:165736723..165738244,2	K562	blood:
5	chr1:165597575..165602245-chr1:165617678..165620274,4	K562	blood:
6	chr1:165598109..165601268-chr1:165795469..165798298,3	MCF-7	breast:
7	chr1:165598557..165602218-chr1:165613054..165616011,3	K562	blood:
8	chr1:165597269..165598908-chr1:165600492..165602238,2	MCF-7	breast:

Variant related genes	Relation type
MGST3	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10800120	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2348733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147591	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4147595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4147597	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147598	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147600	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs6426926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6694924	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9333387	0.82[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6426925	MGST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165594000-165599000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:165595200-165599000	Enhancers	K562	blood
3	chr1:165596000-165599400	Enhancers	Fetal Intestine Small	intestine
4	chr1:165596400-165599400	Enhancers	Fetal Intestine Large	intestine
5	chr1:165597200-165599200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:165597200-165599200	Enhancers	Fetal Heart	heart
7	chr1:165597600-165599000	Enhancers	HepG2	liver
8	chr1:165597800-165599200	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:165597800-165599400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:165598000-165599200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:165598000-165599200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:165598400-165599200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:165598400-165599200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:165598400-165600800	Active TSS	Fetal Brain Male	brain
15	chr1:165598600-165599000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:165598600-165599000	Enhancers	Dnd41	blood
17	chr1:165598600-165599200	Enhancers	Fetal Brain Female	brain
18	chr1:165598600-165599400	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:165598600-165599400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:165598800-165599000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:165598800-165599000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:165598800-165599000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:165598800-165599000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:165598800-165599000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:165598800-165599000	Enhancers	HMEC	breast
26	chr1:165598800-165599200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:165598800-165599200	Enhancers	Stomach Mucosa	stomach
28	chr1:165598800-165599200	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links