Variant report

Variant	rs199498
Chromosome Location	chr17:44865603-44865604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:44862481..44864849-chr17:44865519..44868934,3	K562	blood:
2	chr17:44863317..44866712-chr17:44895110..44898398,4	K562	blood:
3	chr17:44863866..44866478-chr17:44895110..44897062,2	K562	blood:

Variant related genes	Relation type
ENSG00000108379	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 72 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs142167	0.86[GIH][hapmap]
rs169201	0.87[CEU][hapmap]
rs183211	0.86[GIH][hapmap]
rs199436	0.86[GIH][hapmap]
rs199438	0.85[GIH][hapmap]
rs199439	0.88[CEU][hapmap]
rs199442	0.86[GIH][hapmap]
rs199443	0.88[CEU][hapmap]
rs199444	0.85[GIH][hapmap]
rs199445	0.88[CEU][hapmap]
rs199448	0.88[CEU][hapmap]
rs199449	0.86[GIH][hapmap]
rs199451	0.88[CEU][hapmap]
rs199452	0.86[GIH][hapmap]
rs199453	0.86[GIH][hapmap]
rs199454	0.86[GIH][hapmap]
rs199455	0.83[CEU][hapmap]
rs199456	0.88[CEU][hapmap]
rs199457	0.88[CEU][hapmap]
rs199501	0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap]
rs199504	0.90[CEU][hapmap]
rs199505	0.94[CEU][hapmap]
rs199506	0.94[CEU][hapmap]
rs199507	1.00[CEU][hapmap]
rs199509	0.94[CEU][hapmap]
rs199513	0.94[CEU][hapmap]
rs199514	0.94[CEU][hapmap]
rs199515	0.94[CEU][hapmap]
rs199516	0.94[CEU][hapmap]
rs199520	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs199524	0.83[CEU][hapmap]
rs199528	0.94[CEU][hapmap]
rs199533	0.88[CEU][hapmap]
rs199534	0.88[CEU][hapmap]
rs199535	0.88[CEU][hapmap]
rs199536	0.86[GIH][hapmap]
rs2074404	0.83[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs415430	0.94[CEU][hapmap]
rs538628	0.94[CEU][hapmap]
rs70602	0.94[CEU][hapmap]
rs757190	0.91[CHB][hapmap]
rs9896243	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431716	chr17:43893020-44868187	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv431718	chr17:44094463-44873614	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv431729	chr17:44144214-44869063	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv2757660	chr17:44162284-44868187	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv431805	chr17:44165803-44868430	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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	54 gene(s)	inside rSNPs	diseases
6	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv916432	chr17:44223908-44873614	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	esv1819056	chr17:44391822-44873614	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	esv1844763	chr17:44391822-44913631	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv428343	chr17:44391822-44913631	Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	esv1806073	chr17:44443111-44873614	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	esv1850605	chr17:44537030-44913631	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
17	nsv833465	chr17:44706496-44889749	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
18	esv1843460	chr17:44732200-44913631	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Parkinson's disease	24511991	GWAS catalog

mRNA abundance (count:71)

SNP	Gene	Cis/trans	Tissue	Source
rs199498	KANSL1-AS1	cis	Whole Blood	GTEx
rs199498	WNT3	cis	Thyroid	GTEx
rs199498	LRRC37A	cis	Esophagus Muscularis	GTEx
rs199498	LRRC37A2	cis	Stomach	GTEx
rs199498	LRRC37A2	cis	Muscle Skeletal	GTEx
rs199498	MAPK8IP1	trans	lymphoblastoid	RTeQTL
rs199498	LRRC37A17P	cis	Esophagus Mucosa	GTEx
rs199498	RP11-259G18.3	cis	Adipose Subcutaneous	GTEx
rs199498	LRRC37A2	cis	Whole Blood	GTEx
rs199498	RP11-259G18.2	cis	lung	GTEx
rs199498	LRRC37A2	cis	Nerve Tibial	GTEx
rs199498	RP11-259G18.2	cis	Esophagus Mucosa	GTEx
rs199498	LRRC37A4	Cis_chr	lymphoblastoid	RTeQTL
rs199498	RP11-259G18.2	cis	Esophagus Muscularis	GTEx
rs199498	KANSL1-AS1	cis	Heart Left Ventricle	GTEx
rs199498	LOC644246	Cis_1M	lymphoblastoid	RTeQTL
rs199498	LOC644246	cis	uninvolved skin	skin_eQTL
rs199498	RP11-259G18.2	cis	Adipose Subcutaneous	GTEx
rs199498	RP11-259G18.2	cis	Thyroid	GTEx
rs199498	RP11-259G18.3	cis	Artery Aorta	GTEx
rs199498	RP11-259G18.3	cis	Nerve Tibial	GTEx
rs199498	RP11-259G18.2	cis	Whole Blood	GTEx
rs199498	RP11-259G18.3	cis	Muscle Skeletal	GTEx
rs199498	RP11-259G18.3	cis	lung	GTEx
rs199498	LRRC37A2	cis	Artery Tibial	GTEx
rs199498	KANSL1-AS1	cis	Esophagus Muscularis	GTEx
rs199498	KANSL1-AS1	cis	Artery Aorta	GTEx
rs199498	KIAA1267	cis	uninvolved skin	skin_eQTL
rs199498	RP11-259G18.2	cis	Muscle Skeletal	GTEx
rs199498	RP11-259G18.2	cis	Stomach	GTEx
rs199498	LRRC37A	cis	Thyroid	GTEx
rs199498	MAPT	cis	Esophagus Mucosa	GTEx
rs199498	KANSL1-AS1	cis	Stomach	GTEx
rs199498	KANSL1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs199498	LRRC37A2	cis	lung	GTEx
rs199498	LRRC37A	cis	Adipose Subcutaneous	GTEx
rs199498	LRRC37A	cis	Frontal Cortex	GTEx
rs199498	KANSL1-AS1	cis	Artery Tibial	GTEx
rs199498	RP11-259G18.3	cis	Stomach	GTEx
rs199498	LRRC37A	cis	Artery Tibial	GTEx
rs199498	KANSL1-AS1	cis	Thyroid	GTEx
rs199498	RP11-259G18.2	cis	Artery Aorta	GTEx
rs199498	KIAA1267	cis	normal skin	skin_eQTL
rs199498	LRRC37A2	cis	Skin Sun Exposed Lower leg	GTEx
rs199498	RP11-259G18.2	cis	Heart Left Ventricle	GTEx
rs199498	RP11-259G18.3	cis	Esophagus Muscularis	GTEx
rs199498	RP11-259G18.3	cis	Heart Left Ventricle	GTEx
rs199498	RP11-259G18.2	cis	Nerve Tibial	GTEx
rs199498	KANSL1-AS1	cis	Nerve Tibial	GTEx
rs199498	RP11-259G18.3	cis	Artery Tibial	GTEx
rs199498	RP11-259G18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs199498	LOC644246///LOC649063	cis	uninvolved skin	skin_eQTL
rs199498	LRRC37A2	cis	Esophagus Muscularis	GTEx
rs199498	KANSL1-AS1	cis	Adipose Subcutaneous	GTEx
rs199498	RP11-259G18.3	cis	Thyroid	GTEx
rs199498	RP11-259G18.2	cis	Artery Tibial	GTEx
rs199498	RP11-259G18.3	cis	Whole Blood	GTEx
rs199498	LRRC37A	cis	lung	GTEx
rs199498	KANSL1-AS1	cis	Muscle Skeletal	GTEx
rs199498	LRRC37A	cis	Artery Aorta	GTEx
rs199498	RP11-259G18.3	cis	Esophagus Mucosa	GTEx
rs199498	LOC644246///LOC649063	cis	normal skin	skin_eQTL
rs199498	KANSL1-AS1	cis	Esophagus Mucosa	GTEx
rs199498	LRRC37A2	cis	Thyroid	GTEx
rs199498	ARL17	Cis_1M	lymphoblastoid	RTeQTL
rs199498	LOC644246///LOC649063	cis	lesional skin	skin_eQTL
rs199498	MAPK8IP1	cis	Cerebellum	GTEx
rs199498	KANSL1-AS1	cis	lung	GTEx
rs199498	LRRC37A2	cis	Adipose Subcutaneous	GTEx
rs199498	LRRC37A	cis	Nerve Tibial	GTEx
rs199498	RP11-259G18.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:44857000-44866000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:44860400-44866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:44862600-44866000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:44864000-44866000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:44864000-44866600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr17:44864000-44867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:44864000-44870800	Weak transcription	K562	blood
8	chr17:44864200-44866800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:44864200-44871200	Weak transcription	Hela-S3	cervix
10	chr17:44864800-44886600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:44865000-44866400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:44865000-44866600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:44865000-44867600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:44865200-44867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:44865400-44866600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr17:44865600-44865800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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