Variant report

Variant	rs17409195
Chromosome Location	chr22:28638354-28638355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11090520	1.00[AFR][1000 genomes]
rs12484825	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17409164	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4638899	0.85[EUR][1000 genomes]
rs738398	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs738474	1.00[AFR][1000 genomes]
rs9608663	1.00[AFR][1000 genomes]
rs9608666	1.00[AFR][1000 genomes]
rs9608672	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9608675	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9613552	1.00[AFR][1000 genomes]
rs9613558	1.00[AFR][1000 genomes]
rs9613560	1.00[AFR][1000 genomes]
rs9613568	0.90[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs9613569	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs9613573	1.00[ASW][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9613575	0.80[AMR][1000 genomes]
rs9613589	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9613590	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9613591	1.00[AFR][1000 genomes]
rs9613601	0.81[EUR][1000 genomes]
rs9613613	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17409195	HPS4	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28618400-28639600	Weak transcription	Ovary	ovary
2	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
3	chr22:28620400-28639200	Weak transcription	Left Ventricle	heart
4	chr22:28628000-28639400	Weak transcription	Fetal Heart	heart
5	chr22:28628200-28643200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr22:28628600-28639000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:28628600-28640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:28628600-28640800	Weak transcription	NHLF	lung
9	chr22:28631400-28640800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:28632200-28640200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr22:28632400-28640800	Weak transcription	Aorta	Aorta
12	chr22:28633600-28639600	Weak transcription	HSMM	muscle
13	chr22:28633600-28640800	Weak transcription	HSMMtube	muscle
14	chr22:28634200-28640800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:28635600-28650800	Weak transcription	Dnd41	blood
16	chr22:28636400-28640200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:28637600-28638400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr22:28637800-28638400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr22:28638000-28638400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr22:28638000-28638400	Flanking Active TSS	K562	blood
21	chr22:28638200-28638400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr22:28638200-28638400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr22:28638200-28638400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:28638200-28638400	Enhancers	Fetal Brain Male	brain

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