Variant report

Variant	rs17164925
Chromosome Location	chr5:126794256-126794257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11956397	0.87[AMR][1000 genomes]
rs11957319	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17164905	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17164911	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17164941	0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17164956	0.87[AMR][1000 genomes]
rs17164963	0.87[AMR][1000 genomes]
rs17763126	1.00[JPT][hapmap]
rs2408871	0.88[YRI][hapmap]
rs55851028	0.87[AMR][1000 genomes]
rs56853109	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57502023	0.87[AMR][1000 genomes]
rs58718502	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59739975	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60678437	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60694077	0.87[AMR][1000 genomes]
rs60931267	0.87[AMR][1000 genomes]
rs61021426	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61031224	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73331252	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346997	0.87[AMR][1000 genomes]
rs73348707	0.87[AMR][1000 genomes]
rs73348729	0.87[AMR][1000 genomes]
rs73348755	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73348768	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348777	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126774600-126798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:126778000-126795400	Weak transcription	Brain Angular Gyrus	brain
3	chr5:126781800-126794800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:126782600-126795200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:126783400-126795600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:126783800-126797200	Weak transcription	HSMM	muscle
7	chr5:126785200-126797000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:126785400-126794800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:126786000-126797600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:126788800-126797800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:126789400-126797000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:126789800-126797000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:126790200-126797200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:126791400-126797200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:126792800-126795600	Strong transcription	HSMMtube	muscle
17	chr5:126793200-126798000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:126793400-126796800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:126793400-126797000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:126793400-126797000	Weak transcription	Brain Anterior Caudate	brain
21	chr5:126793400-126797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:126793400-126799600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:126793400-126805200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:126793800-126795400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:126794000-126797000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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