Variant report

Variant	rs6005790
Chromosome Location	chr22:28876170-28876171
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs134522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs134527	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs134544	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs134551	0.81[CEU][hapmap]
rs2346397	0.84[CEU][hapmap]
rs5752746	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs5762670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695267	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs695318	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs695388	0.85[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs695459	0.92[ASN][1000 genomes]
rs695567	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs695629	0.85[AMR][1000 genomes]
rs695700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs695709	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs737622	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738199	0.90[JPT][hapmap]
rs9613609	0.81[AMR][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	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6005790	TTC28	cis	cerebellum	SCAN
rs6005790	TTC28	cis	lymphoblastoid	seeQTL
rs6005790	SRRD	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28861600-28880200	Weak transcription	Ovary	ovary
2	chr22:28874000-28878600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28874800-28876600	Enhancers	Dnd41	blood
4	chr22:28875000-28879000	Enhancers	Fetal Brain Male	brain
5	chr22:28875200-28878000	Enhancers	Fetal Lung	lung
6	chr22:28875600-28876400	Enhancers	Fetal Stomach	stomach
7	chr22:28875800-28878400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr22:28876000-28876600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr22:28876000-28876600	Enhancers	Brain Hippocampus Middle	brain
10	chr22:28876000-28876600	Flanking Active TSS	Fetal Brain Female	brain
11	chr22:28876000-28876800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr22:28876000-28876800	Enhancers	Brain Cingulate Gyrus	brain
13	chr22:28876000-28877000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:28876000-28877200	Enhancers	Fetal Kidney	kidney
15	chr22:28876000-28878000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr22:28876000-28878000	Enhancers	Brain Germinal Matrix	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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