Variant report

Variant	rs1878589
Chromosome Location	chr2:99517979-99517980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99513625..99516129-chr2:99517702..99519435,2	K562	blood:
2	chr2:99484326..99485994-chr2:99516772..99518470,2	MCF-7	breast:
3	chr2:99514955..99516765-chr2:99517023..99518903,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10175560	0.81[EUR][1000 genomes]
rs10192266	0.86[EUR][1000 genomes]
rs11123756	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11900176	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs11900524	0.81[EUR][1000 genomes]
rs12464134	0.89[ASN][1000 genomes]
rs12467504	0.89[EUR][1000 genomes]
rs12474283	0.85[CEU][hapmap]
rs12478574	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12712034	0.84[EUR][1000 genomes]
rs12712037	0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs12712039	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12712040	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712042	0.86[EUR][1000 genomes]
rs12990579	0.89[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs13004700	0.85[CEU][hapmap]
rs13005124	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs13005148	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13006398	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13024838	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028500	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1581249	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17758170	1.00[CEU][hapmap];0.94[CHB][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949424	0.83[EUR][1000 genomes]
rs1962029	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2048949	0.83[EUR][1000 genomes]
rs4311103	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4499468	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4553869	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4850890	0.86[EUR][1000 genomes]
rs4851174	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs4851175	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4851176	0.86[EUR][1000 genomes]
rs6542841	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6542845	0.86[EUR][1000 genomes]
rs6704682	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6724477	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6741166	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6742047	0.86[EUR][1000 genomes]
rs6752025	0.85[EUR][1000 genomes]
rs6757098	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6760065	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7423519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565510	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7565614	0.81[EUR][1000 genomes]
rs7565736	0.80[EUR][1000 genomes]
rs7565819	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588441	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590596	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7593332	0.83[EUR][1000 genomes]
rs883773	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs925887	0.92[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
rs1878589	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99511200-99520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
3	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:99513400-99520600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:99515200-99524600	Weak transcription	Pancreas	Pancrea
6	chr2:99515800-99520600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:99517600-99526000	Weak transcription	Gastric	stomach

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