Variant report

Variant	rs16976888
Chromosome Location	chr15:56677586-56677587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1068681	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1074018	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087764	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1087765	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1356863	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1365164	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1402172	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1582756	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976893	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194942	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2465972	0.80[ASN][1000 genomes]
rs2554289	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2554290	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2554291	0.88[ASN][1000 genomes]
rs2554292	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2554293	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2554294	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682020	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2682028	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682035	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682036	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682037	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682039	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682042	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682052	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682063	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2682068	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2713901	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2713903	0.92[YRI][hapmap]
rs2713915	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2713920	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2713928	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2718903	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2718911	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2718916	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2718929	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2718931	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2718932	0.80[ASN][1000 genomes]
rs2718940	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2718946	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2718948	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2725845	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725865	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725866	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725868	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2725869	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28369022	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408440	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28545512	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567497	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28572531	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28609291	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28678726	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28714692	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28721891	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28756289	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28790092	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28790997	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28801764	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28878210	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28895874	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3985756	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3985760	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705451	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724099	0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795778	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795779	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs795789	0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795794	0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795795	1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795796	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795798	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs797066	0.89[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs808731	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs811257	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9920137	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904246	chr15:56665827-56732192	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56664400-56685200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr15:56665200-56733400	Weak transcription	Fetal Kidney	kidney
3	chr15:56672000-56694600	Weak transcription	Ovary	ovary
4	chr15:56673000-56678000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:56675000-56685000	Weak transcription	Fetal Intestine Small	intestine
6	chr15:56675400-56678600	Weak transcription	Thymus	Thymus
7	chr15:56675400-56691000	Weak transcription	Fetal Stomach	stomach
8	chr15:56676200-56677600	Strong transcription	Fetal Lung	lung
9	chr15:56676400-56678600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:56676400-56687400	Weak transcription	A549	lung
11	chr15:56676600-56677600	ZNF genes & repeats	GM12878-XiMat	blood
12	chr15:56676600-56678800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:56676800-56677800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:56676800-56678800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:56677200-56691800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:56677400-56677800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:56677400-56678000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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