Variant report

Variant	rs8180562
Chromosome Location	chr6:28141460-28141461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28114023..28116514-chr6:28140821..28142686,2	K562	blood:
2	chr6:28140632..28142343-chr6:28159813..28161834,2	K562	blood:
3	chr6:28139929..28141962-chr6:28142332..28144610,2	K562	blood:
4	chr6:28141218..28142737-chr6:28303339..28305763,2	K562	blood:
5	chr6:28139078..28141804-chr6:28165060..28166721,2	K562	blood:
6	chr6:27858835..27861043-chr6:28141226..28144128,2	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000216901	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12055625	0.82[ASN][1000 genomes]
rs1321504	0.82[ASN][1000 genomes]
rs1321505	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13437126	0.97[ASN][1000 genomes]
rs13437444	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16893735	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34130214	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34712084	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734571	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3757188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713138	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4713139	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713140	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs735765	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348792	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9357064	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9366717	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9368560	0.90[ASN][1000 genomes]
rs9368561	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380069	0.80[EUR][1000 genomes]
rs9393889	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9393902	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9393908	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9461432	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461439	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468287	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468300	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468301	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8180562	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs8180562	AL022393.7	cis	Muscle Skeletal	GTEx
rs8180562	RP5-874C20.3	cis	Thyroid	GTEx
rs8180562	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs8180562	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28129800-28142200	Weak transcription	Aorta	Aorta
2	chr6:28129800-28145400	Weak transcription	Brain Angular Gyrus	brain
3	chr6:28130000-28142600	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:28130200-28141800	Weak transcription	Fetal Kidney	kidney
5	chr6:28130200-28142800	Weak transcription	Left Ventricle	heart
6	chr6:28130400-28142600	Weak transcription	Psoas Muscle	Psoas
7	chr6:28130600-28141800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:28135800-28141600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:28138000-28145600	Weak transcription	K562	blood
10	chr6:28139000-28144400	Weak transcription	Brain Anterior Caudate	brain
11	chr6:28139400-28141800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:28139400-28145600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:28140200-28142400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:28140800-28142400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:28141000-28143200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links