Variant report

Variant	rs17540415
Chromosome Location	chr8:90558935-90558936
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10081423	0.84[EUR][1000 genomes]
rs10081569	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10087963	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10091099	0.81[EUR][1000 genomes]
rs10092477	0.85[EUR][1000 genomes]
rs10093582	0.81[EUR][1000 genomes]
rs10095948	0.84[EUR][1000 genomes]
rs10103261	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10103816	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10103935	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10104048	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10956130	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10956137	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11775122	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11990948	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11992806	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11996000	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12549527	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13258962	0.86[EUR][1000 genomes]
rs1386648	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1487670	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1487678	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1510465	0.88[EUR][1000 genomes]
rs1546745	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1601766	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1601767	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17840661	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996853	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28452224	0.82[AMR][1000 genomes]
rs28678004	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs311638	0.85[EUR][1000 genomes]
rs34871636	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35261547	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35285023	0.84[EUR][1000 genomes]
rs4563939	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4571769	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4576465	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4960972	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4960973	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961142	0.86[EUR][1000 genomes]
rs4961147	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56135833	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6470130	0.86[EUR][1000 genomes]
rs6981677	0.85[EUR][1000 genomes]
rs6986107	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6995460	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6999527	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs719239	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7844045	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9297665	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9297679	0.85[EUR][1000 genomes]
rs9987398	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2761173	chr8:90404592-90592009	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1027327	chr8:90426338-90585108	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1028969	chr8:90475194-90650295	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv528988	chr8:90475375-90608246	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv611720	chr8:90476925-90608246	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv427825	chr8:90495139-90653696	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv527244	chr8:90532927-90589630	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv870380	chr8:90546585-90720182	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv2761447	chr8:90553156-90576196	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1028026	chr8:90553930-90678631	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv982109	chr8:90556188-90703631	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv1026523	chr8:90558935-90722580	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90556800-90559000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:90558000-90559000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:90558000-90559200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:90558000-90559400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr8:90558000-90559400	Enhancers	HMEC	breast
6	chr8:90558000-90560000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:90558200-90559400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:90558200-90559400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:90558200-90559400	Enhancers	NHEK	skin
10	chr8:90558200-90559600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:90558200-90559600	Enhancers	NH-A	brain
12	chr8:90558200-90559800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr8:90558400-90559400	Enhancers	HUVEC	blood vessel
14	chr8:90558400-90559600	Enhancers	Osteobl	bone
15	chr8:90558400-90559800	Enhancers	Hela-S3	cervix
16	chr8:90558600-90559200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:90558600-90559200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr8:90558600-90559200	Flanking Active TSS	A549	lung
19	chr8:90558600-90559400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:90558600-90559400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr8:90558600-90559400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:90558600-90559400	Enhancers	Rectal Smooth Muscle	rectum
23	chr8:90558600-90559400	Enhancers	HSMM	muscle
24	chr8:90558600-90559600	Enhancers	NHDF-Ad	bronchial
25	chr8:90558800-90559000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:90558800-90559200	Weak transcription	NHLF	lung

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