Variant report

Variant	rs17454420
Chromosome Location	chr5:152014941-152014942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:152014610..152016353-chr5:152016707..152018951,3	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10155517	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10515675	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10515676	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11167584	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956651	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12188564	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13359939	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361438	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17452991	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17453481	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17453530	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17453740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453880	0.81[AMR][1000 genomes]
rs17455800	0.87[EUR][1000 genomes]
rs17549307	1.00[AFR][1000 genomes]
rs17549488	1.00[AFR][1000 genomes]
rs17550343	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565365	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565470	0.87[EUR][1000 genomes]
rs17565505	0.85[EUR][1000 genomes]
rs17565693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2961756	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2961760	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2961765	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2961766	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964230	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964231	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3923209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4246030	1.00[AFR][1000 genomes]
rs4246033	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4342320	0.87[AFR][1000 genomes]
rs4398624	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4406125	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4478308	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4484412	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4557395	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4580766	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958316	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958317	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958320	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958551	1.00[AFR][1000 genomes]
rs4958554	1.00[AFR][1000 genomes]
rs4958555	1.00[AFR][1000 genomes]
rs4958560	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958561	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4958562	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4958564	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958566	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958567	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4958568	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958569	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55648729	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55696164	1.00[AFR][1000 genomes]
rs55786399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56014830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56050684	1.00[AFR][1000 genomes]
rs57358310	0.81[AMR][1000 genomes]
rs67979431	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871699	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6871986	0.81[AMR][1000 genomes]
rs6876403	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6876723	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6884556	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6895969	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72795336	1.00[AFR][1000 genomes]
rs72795340	1.00[AFR][1000 genomes]
rs72795344	1.00[AFR][1000 genomes]
rs72795349	0.87[AFR][1000 genomes]
rs72795350	0.87[AFR][1000 genomes]
rs72795351	0.87[AFR][1000 genomes]
rs72795352	0.87[AFR][1000 genomes]
rs72795364	1.00[AFR][1000 genomes]
rs72795366	1.00[AFR][1000 genomes]
rs72795376	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72795379	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72795389	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72797226	1.00[ASN][1000 genomes]
rs72797233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797241	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797251	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72797254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797262	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72797296	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799113	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324734	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv5074	chr5:152010691-152055779	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17454420	GLRA1	cis	cerebellum	SCAN
rs17454420	SLC26A2	cis	cerebellum	SCAN
rs17454420	GPX3	cis	cerebellum	SCAN
rs17454420	IL17B	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152008400-152022800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:152009000-152016800	Enhancers	Fetal Brain Female	brain
3	chr5:152011800-152021800	Weak transcription	Aorta	Aorta
4	chr5:152012800-152018000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:152013400-152015000	Enhancers	Brain Hippocampus Middle	brain
6	chr5:152013400-152015200	Enhancers	Brain Germinal Matrix	brain
7	chr5:152013400-152015400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:152013600-152015000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:152013600-152015400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:152013600-152018400	Weak transcription	Fetal Lung	lung
11	chr5:152013800-152015000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:152013800-152015000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr5:152013800-152015200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:152014000-152015000	Enhancers	Brain Cingulate Gyrus	brain
15	chr5:152014000-152015000	Enhancers	Brain Substantia Nigra	brain
16	chr5:152014200-152015200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:152014400-152015000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:152014600-152018400	Weak transcription	Adipose Nuclei	Adipose
19	chr5:152014800-152021000	Weak transcription	Fetal Brain Male	brain

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