Variant report

Variant	rs4538475
Chromosome Location	chr4:15737937-15737938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15655679..15657937-chr4:15737188..15739918,2	K562	blood:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10516290	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10516291	0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1058212	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11724635	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11931532	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11934811	0.92[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11943501	1.00[CEU][hapmap]
rs11944132	0.91[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12640554	0.82[ASN][1000 genomes]
rs12640596	0.83[ASN][1000 genomes]
rs12643722	0.82[ASN][1000 genomes]
rs12644354	0.82[ASN][1000 genomes]
rs12645513	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12645693	0.91[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12646331	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12651052	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12651490	0.81[ASN][1000 genomes]
rs16892271	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs16892272	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16892276	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16892283	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16892287	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs16892289	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs16898413	0.81[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs36097300	0.80[ASN][1000 genomes]
rs3900588	0.92[CEU][hapmap]
rs4266290	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4273468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292325	0.84[CEU][hapmap]
rs4320134	0.92[CEU][hapmap]
rs4321629	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4328911	0.83[ASN][1000 genomes]
rs4336219	0.83[ASN][1000 genomes]
rs4336220	0.83[ASN][1000 genomes]
rs4342183	0.84[ASN][1000 genomes]
rs4435745	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4498133	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4588454	0.83[CEU][hapmap]
rs4613561	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4698119	0.82[JPT][hapmap]
rs4698412	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4698413	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs56381553	0.81[ASN][1000 genomes]
rs57326588	0.81[ASN][1000 genomes]
rs57497036	0.80[ASN][1000 genomes]
rs58335439	0.81[ASN][1000 genomes]
rs58978163	0.80[ASN][1000 genomes]
rs59919329	0.83[ASN][1000 genomes]
rs60913985	0.81[ASN][1000 genomes]
rs6835705	0.91[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6844968	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs73123615	0.81[ASN][1000 genomes]
rs73123625	0.83[ASN][1000 genomes]
rs73125993	0.83[ASN][1000 genomes]
rs955410	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs955411	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs9790535	0.83[ASN][1000 genomes]
rs9790554	0.83[ASN][1000 genomes]
rs9790670	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Parkinson's disease	19915576	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4538475	TIMM10	trans	parietal	SCAN
rs4538475	NCAPG	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:15708800-15739400	Weak transcription	Ovary	ovary
3	chr4:15723000-15743000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:15723000-15744600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:15726000-15740200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:15727400-15740400	Weak transcription	Fetal Intestine Large	intestine
7	chr4:15729000-15743200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:15732000-15738800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:15733600-15742800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:15735400-15739000	Weak transcription	Fetal Intestine Small	intestine
11	chr4:15735400-15742800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:15735800-15740200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr4:15736400-15739000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:15736400-15739200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:15736600-15739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:15737200-15738400	Weak transcription	Dnd41	blood
17	chr4:15737400-15739000	Weak transcription	Fetal Thymus	thymus
18	chr4:15737800-15738000	Enhancers	Brain Anterior Caudate	brain
19	chr4:15737800-15739200	Enhancers	Primary B cells from peripheral blood	blood
20	chr4:15737800-15740400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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