Variant report

Variant	rs2468129
Chromosome Location	chr15:76843212-76843213
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12442966	0.88[EUR][1000 genomes]
rs1443110	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs157757	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157758	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157760	0.82[AFR][1000 genomes]
rs157761	0.82[AFR][1000 genomes]
rs157768	0.91[AFR][1000 genomes]
rs157778	0.82[AFR][1000 genomes]
rs157788	0.91[AFR][1000 genomes]
rs157789	0.91[AFR][1000 genomes]
rs166794	0.85[EUR][1000 genomes]
rs1905694	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs203753	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2170998	0.82[EUR][1000 genomes]
rs2439982	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439984	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439989	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439991	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439992	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439993	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454453	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2459360	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2459363	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468113	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468116	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468120	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468122	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468123	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469241	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469242	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2585730	0.85[EUR][1000 genomes]
rs2629021	0.85[EUR][1000 genomes]
rs2629025	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs279997	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs279999	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280001	0.82[EUR][1000 genomes]
rs280005	0.82[EUR][1000 genomes]
rs280008	0.82[EUR][1000 genomes]
rs280012	0.85[EUR][1000 genomes]
rs280013	0.85[EUR][1000 genomes]
rs280014	0.85[EUR][1000 genomes]
rs283799	0.82[AFR][1000 genomes]
rs283802	0.82[AFR][1000 genomes]
rs284885	0.81[AFR][1000 genomes]
rs284897	0.82[AFR][1000 genomes]
rs284898	0.82[AFR][1000 genomes]
rs284903	0.82[AFR][1000 genomes]
rs284904	0.82[AFR][1000 genomes]
rs2930681	0.85[EUR][1000 genomes]
rs35994108	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs387321	0.82[AFR][1000 genomes]
rs506000	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2468129	ISL2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76805600-76845800	Weak transcription	Primary T cells from cord blood	blood
2	chr15:76842000-76844200	Weak transcription	Fetal Stomach	stomach
3	chr15:76842200-76845400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:76842400-76845600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:76842600-76845400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:76842600-76845600	Weak transcription	Lung	lung
7	chr15:76842600-76845800	Weak transcription	Spleen	Spleen
8	chr15:76842800-76846200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:76843000-76844200	Weak transcription	Fetal Intestine Small	intestine
10	chr15:76843000-76844600	Weak transcription	Pancreas	Pancrea
11	chr15:76843000-76845400	Weak transcription	Left Ventricle	heart
12	chr15:76843000-76853400	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:76843200-76844800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:76843200-76845200	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:76843200-76845400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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