Variant report

Variant	rs13006398
Chromosome Location	chr2:99522323-99522324
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10192266	0.83[EUR][1000 genomes]
rs11123756	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12464134	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12467504	0.86[EUR][1000 genomes]
rs12478574	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12712039	0.81[AMR][1000 genomes]
rs12712040	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712042	0.83[EUR][1000 genomes]
rs13005124	0.82[EUR][1000 genomes]
rs13005148	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13024838	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13028500	0.80[EUR][1000 genomes]
rs1581249	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17758170	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1878589	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962029	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2048949	0.81[EUR][1000 genomes]
rs4311103	0.83[EUR][1000 genomes]
rs4499468	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4553869	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4850890	0.83[EUR][1000 genomes]
rs4851174	0.83[EUR][1000 genomes]
rs4851175	0.83[EUR][1000 genomes]
rs4851176	0.83[EUR][1000 genomes]
rs6542841	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6542845	0.82[EUR][1000 genomes]
rs6704682	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6724477	0.83[EUR][1000 genomes]
rs6741166	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6742047	0.83[EUR][1000 genomes]
rs6752025	0.81[EUR][1000 genomes]
rs6757098	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6760065	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7423519	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565510	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7565819	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7588441	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590596	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs883773	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13006398	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
2	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:99515200-99524600	Weak transcription	Pancreas	Pancrea
4	chr2:99517600-99526000	Weak transcription	Gastric	stomach
5	chr2:99518800-99525000	Weak transcription	Spleen	Spleen
6	chr2:99519600-99524800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:99520400-99522400	Weak transcription	Fetal Brain Male	brain
8	chr2:99520800-99528600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:99521000-99525000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:99521000-99525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:99521000-99525000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:99521000-99525200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:99521000-99526000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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