Variant report

Variant	rs12712040
Chromosome Location	chr2:99513416-99513417
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99511094..99513536-chr2:99513971..99515914,2	MCF-7	breast:
2	chr2:99505531..99508517-chr2:99513277..99515165,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10175560	0.86[EUR][1000 genomes]
rs10192266	0.81[EUR][1000 genomes]
rs11123756	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11900176	0.83[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11900524	0.86[EUR][1000 genomes]
rs12464134	0.82[ASN][1000 genomes]
rs12467504	0.85[EUR][1000 genomes]
rs12478574	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12712033	0.82[EUR][1000 genomes]
rs12712034	0.89[EUR][1000 genomes]
rs12712037	0.89[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12712042	0.81[EUR][1000 genomes]
rs12990579	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs13005124	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs13005148	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13006398	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13024838	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13028500	0.87[CEU][hapmap]
rs1581249	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17758170	0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1878589	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1949424	0.89[EUR][1000 genomes]
rs1962029	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4311103	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4499468	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4553869	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4850890	0.81[EUR][1000 genomes]
rs4851174	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4851175	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4851176	0.81[EUR][1000 genomes]
rs6542841	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6542845	0.81[EUR][1000 genomes]
rs6704682	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6724477	0.91[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6741166	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6742047	0.81[EUR][1000 genomes]
rs6752025	0.90[EUR][1000 genomes]
rs6757098	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6760065	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7423519	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7565510	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7565614	0.86[EUR][1000 genomes]
rs7565736	0.86[EUR][1000 genomes]
rs7565819	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7588441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7590596	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7593332	0.89[EUR][1000 genomes]
rs883773	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs925887	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12712040	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99500000-99517000	Weak transcription	Gastric	stomach
2	chr2:99511200-99520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99511800-99513600	Enhancers	Fetal Muscle Leg	muscle
4	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
5	chr2:99512200-99513800	Enhancers	HSMMtube	muscle
6	chr2:99513200-99515000	Weak transcription	Pancreas	Pancrea
7	chr2:99513200-99515400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:99513400-99520600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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