Variant report

Variant	rs17416642
Chromosome Location	chr1:57471621-57471622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11811443	0.93[EUR][1000 genomes]
rs1342432	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114796	0.96[EUR][1000 genomes]
rs17416655	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17417626	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17449278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17450593	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17450764	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17451933	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs41286862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57172704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57655464	1.00[EUR][1000 genomes]
rs59236630	0.96[EUR][1000 genomes]
rs6698886	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706354	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706355	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706359	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74077326	1.00[EUR][1000 genomes]
rs7514916	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs835446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs835902	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9651187	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17416642	MSC	trans	brain	seeQTL
rs17416642	PIP4K2B	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57457800-57480400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57459000-57474600	Weak transcription	Fetal Brain Female	brain
3	chr1:57460400-57483000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:57463800-57482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:57464200-57473200	Weak transcription	Fetal Heart	heart
6	chr1:57466800-57473800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:57466800-57474000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:57468800-57475200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57468800-57477400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:57469000-57471800	Weak transcription	Fetal Intestine Large	intestine
11	chr1:57469800-57472800	Weak transcription	HepG2	liver
12	chr1:57469800-57477200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:57470200-57473200	Weak transcription	Liver	Liver
14	chr1:57471200-57482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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