Variant report

Variant	rs6738069
Chromosome Location	chr2:39150059-39150060
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39106547..39110069-chr2:39150032..39154401,3	K562	blood:
2	chr2:38975236..38979856-chr2:39147860..39151897,5	K562	blood:
3	chr2:39106402..39108515-chr2:39149048..39151113,2	MCF-7	breast:
4	chr2:39145069..39147790-chr2:39148985..39151142,2	MCF-7	breast:
5	chr2:39147727..39150227-chr2:39155221..39157065,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000214694	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1010859	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10181808	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10204999	0.96[EUR][1000 genomes]
rs11124654	0.82[EUR][1000 genomes]
rs1131752	0.81[EUR][1000 genomes]
rs11681583	0.94[ASN][1000 genomes]
rs11689954	0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs12621073	0.88[EUR][1000 genomes]
rs12712626	0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]
rs12712628	0.82[EUR][1000 genomes]
rs13035182	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17422748	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099940	0.81[EUR][1000 genomes]
rs3099941	0.91[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3099942	0.91[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs3099945	0.88[GIH][hapmap];0.85[MEX][hapmap]
rs3099956	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3099957	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs3099958	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099959	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3099998	0.82[EUR][1000 genomes]
rs3100000	0.86[ASN][1000 genomes]
rs3112159	0.81[CHB][hapmap];0.82[GIH][hapmap]
rs3112163	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs3112166	0.84[ASN][1000 genomes]
rs3112175	0.92[ASN][1000 genomes]
rs3112191	0.88[JPT][hapmap]
rs373300	0.81[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs384007	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs384421	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs389023	0.91[EUR][1000 genomes]
rs3923144	0.88[CHD][hapmap];0.88[GIH][hapmap]
rs434696	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4602206	0.89[JPT][hapmap]
rs4670266	0.81[CHB][hapmap]
rs4670268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670899	0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs4670900	0.83[ASN][1000 genomes]
rs6544180	0.87[EUR][1000 genomes]
rs6706091	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs6744514	0.82[EUR][1000 genomes]
rs6754902	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7565111	0.81[CHB][hapmap]
rs8179664	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9808136	0.82[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6738069	ITGB1	trans	parietal	SCAN
rs6738069	DHX57	cis	cerebellum	SCAN
rs6738069	MORN2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39143000-39151000	Weak transcription	Brain Angular Gyrus	brain
3	chr2:39143800-39164600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:39145800-39172800	Weak transcription	Lung	lung
5	chr2:39147000-39166600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:39147800-39150400	Enhancers	HepG2	liver
7	chr2:39149000-39164800	Weak transcription	Ovary	ovary
8	chr2:39149600-39150600	Enhancers	Fetal Heart	heart
9	chr2:39149600-39150600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:39150000-39150200	Enhancers	Right Ventricle	heart
11	chr2:39150000-39150200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr2:39150000-39150400	Enhancers	Psoas Muscle	Psoas
13	chr2:39150000-39186600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links