Variant report

Variant	rs17417060
Chromosome Location	chr10:45412777-45412778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11239287	0.93[ASN][1000 genomes]
rs11595747	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11598392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1332628	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs17515726	0.89[ASN][1000 genomes]
rs72778871	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72780637	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs949607	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs952956	1.00[CHB][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517161	chr10:45210690-45416256	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv466909	chr10:45408011-45446791	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550714	chr10:45408011-45446791	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2762860	chr10:45411165-45412956	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17417060	ZNF488	cis	parietal	SCAN
rs17417060	HNRNPA3P1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45401400-45415600	Weak transcription	Fetal Brain Female	brain
2	chr10:45406400-45419000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:45407800-45422800	Weak transcription	Ovary	ovary
4	chr10:45408600-45417200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:45409600-45412800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:45410000-45412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:45410000-45419000	Weak transcription	Pancreas	Pancrea
8	chr10:45410200-45430400	Weak transcription	Gastric	stomach
9	chr10:45410600-45419600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:45411000-45413000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:45412400-45412800	Weak transcription	Fetal Kidney	kidney
12	chr10:45412400-45413000	Enhancers	Fetal Heart	heart
13	chr10:45412600-45413400	Strong transcription	Rectal Mucosa Donor 29	rectum

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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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