Variant report

Variant	rs17660319
Chromosome Location	chr19:52053130-52053131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12972180	0.82[JPT][hapmap]
rs12972472	0.82[JPT][hapmap]
rs1466302	0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1551159	0.88[ASN][1000 genomes]
rs16982810	0.81[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17660341	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17716726	0.96[ASN][1000 genomes]
rs2168638	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2168639	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4289096	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73050804	0.96[ASN][1000 genomes]
rs73050815	0.88[ASN][1000 genomes]
rs73067339	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73067342	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73067352	0.96[ASN][1000 genomes]
rs73067368	0.96[ASN][1000 genomes]
rs73067369	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17660319	SIGLEC5	cis	lymphoblastoid	seeQTL
rs17660319	ZNF416	cis	parietal	SCAN
rs17660319	ZNF175	cis	lymphoblastoid	seeQTL
rs17660319	ZNF880	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52048800-52058000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:52050400-52053400	Flanking Active TSS	K562	blood
3	chr19:52050400-52053600	Enhancers	Primary T cells from cord blood	blood
4	chr19:52050600-52054000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:52050600-52054400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
6	chr19:52051000-52053400	Enhancers	Primary hematopoietic stem cells	blood
7	chr19:52051800-52053200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:52052000-52053600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr19:52052200-52053600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr19:52052200-52053600	Flanking Active TSS	GM12878-XiMat	blood
11	chr19:52052400-52053600	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr19:52052600-52053600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
13	chr19:52052800-52056400	Weak transcription	Spleen	Spleen
14	chr19:52053000-52053200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:52053000-52053400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:52053000-52053400	Bivalent Enhancer	Stomach Mucosa	stomach

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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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