Variant report

Variant	rs339693
Chromosome Location	chr3:42738039-42738040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42737037..42739602-chr3:42741625..42745097,3	K562	blood:
2	chr3:42725723..42728637-chr3:42737292..42738802,2	K562	blood:
3	chr3:42731871..42735577-chr3:42735978..42742052,8	K562	blood:

Variant related genes	Relation type
ENSG00000230970	Chromatin interaction
ENSG00000157119	Chromatin interaction
ENSG00000010282	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11079	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs12485678	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12486439	0.86[ASN][1000 genomes]
rs12488174	0.83[ASN][1000 genomes]
rs12490743	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12492886	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12493321	0.83[ASN][1000 genomes]
rs12495805	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13061576	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13064320	0.83[ASN][1000 genomes]
rs13085272	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13090185	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13095730	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1871121	0.84[ASN][1000 genomes]
rs2290972	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2290973	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2372111	0.83[ASN][1000 genomes]
rs2372114	0.83[ASN][1000 genomes]
rs339694	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs339695	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339696	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339697	0.82[ASW][hapmap];0.96[CEU][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34025253	0.83[ASN][1000 genomes]
rs34188562	0.86[ASN][1000 genomes]
rs34378441	0.96[EUR][1000 genomes]
rs34482203	0.83[ASN][1000 genomes]
rs34510173	0.83[ASN][1000 genomes]
rs34648075	0.83[ASN][1000 genomes]
rs35389123	0.86[ASN][1000 genomes]
rs35647815	0.84[ASN][1000 genomes]
rs35697625	0.83[ASN][1000 genomes]
rs35766391	0.83[ASN][1000 genomes]
rs36061398	0.83[ASN][1000 genomes]
rs3846062	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs3912102	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3912103	0.86[ASN][1000 genomes]
rs4488806	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs55799024	0.86[ASN][1000 genomes]
rs56232384	0.86[ASN][1000 genomes]
rs56978598	0.86[ASN][1000 genomes]
rs62246602	0.86[ASN][1000 genomes]
rs62246607	0.83[ASN][1000 genomes]
rs62250122	0.86[ASN][1000 genomes]
rs66665035	0.97[ASN][1000 genomes]
rs6765740	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7429327	0.84[ASN][1000 genomes]
rs7617368	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs339693	TMEM42	cis	parietal	SCAN
rs339693	HIGD1A	cis	parietal	SCAN
rs339693	HHATL	cis	parietal	SCAN
rs339693	CCDC13-AS1	cis	Thyroid	GTEx
rs339693	HHATL	cis	cerebellum	SCAN
rs339693	CCDC13	cis	Thyroid	GTEx
rs339693	EXOSC7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42728000-42742800	Weak transcription	Gastric	stomach
2	chr3:42733600-42740800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:42734200-42738800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:42734400-42738200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:42734800-42740800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:42736600-42738200	Strong transcription	Brain Hippocampus Middle	brain
7	chr3:42736800-42738600	Enhancers	Fetal Heart	heart
8	chr3:42736800-42738800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:42737000-42740800	Enhancers	Right Ventricle	heart
10	chr3:42737600-42738400	Strong transcription	Brain Anterior Caudate	brain
11	chr3:42737600-42738400	Strong transcription	Brain Substantia Nigra	brain
12	chr3:42737600-42738800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:42737800-42738600	Weak transcription	Right Atrium	heart
14	chr3:42737800-42739200	Enhancers	Left Ventricle	heart
15	chr3:42738000-42738800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links