Variant report

Variant	rs17419873
Chromosome Location	chr1:57570518-57570519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12405609	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12406184	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12407883	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12564961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114978	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115023	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115030	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17420013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17420181	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17420216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35522019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55706301	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61765294	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765295	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765320	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6697173	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs728719	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17419873	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57567000-57570800	Enhancers	Fetal Heart	heart
3	chr1:57567400-57576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57567600-57570800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:57568400-57571200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:57569000-57570600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57569200-57570600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:57569200-57570800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:57569200-57571200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:57569200-57571200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:57569200-57571800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:57569200-57574200	Weak transcription	Right Atrium	heart
13	chr1:57569400-57571000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:57569400-57573600	Weak transcription	Ovary	ovary
15	chr1:57569400-57574400	Weak transcription	Left Ventricle	heart
16	chr1:57569600-57570600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:57569800-57571000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:57569800-57571200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:57570200-57570600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:57570400-57571600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:57570400-57572000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:57570400-57572200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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