Variant report

Variant	rs6043363
Chromosome Location	chr20:15542612-15542613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr20:15542460-15542795	K562	blood:	n/a	chr20:15542612-15542630 chr20:15542611-15542625
2	MAFK	chr20:15542429-15542822	H1-hESC	embryonic stem cell:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
3	ATF2	chr20:15542293-15542732	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXP2	chr20:15542350-15542620	SK-N-MC	brain:	n/a	n/a
5	MAFK	chr20:15542431-15542804	HepG2	liver:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
6	RFX5	chr20:15542603-15542650	HepG2	liver:	n/a	n/a
7	HDAC2	chr20:15542324-15542672	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr20:15542295-15542615	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr20:15542370-15542723	SK-N-MC	brain:	n/a	n/a
10	MAFK	chr20:15542433-15542804	IMR90	lung:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
11	MAFK	chr20:15542346-15542898	GM12878	blood:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
12	MAFK	chr20:15542457-15542783	K562	blood:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
13	MAFK	chr20:15542471-15542777	Hela-S3	cervix:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626
14	MAFF	chr20:15542430-15542808	HepG2	liver:	n/a	chr20:15542612-15542630 chr20:15542611-15542625
15	MAFK	chr20:15542434-15542803	HepG2	liver:	n/a	chr20:15542611-15542625 chr20:15542608-15542628 chr20:15542615-15542624 chr20:15542613-15542628 chr20:15542614-15542624 chr20:15542610-15542626

Variant related genes	Relation type
ENSG00000212111	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1017165	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1035178	0.89[CHB][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233732	1.00[GIH][hapmap];0.88[TSI][hapmap]
rs16995959	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6074913	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6074914	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6074916	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6079873	0.88[JPT][hapmap]
rs62195614	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62195615	0.88[EUR][1000 genomes];0.90[ASN][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	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2751909	chr20:15489871-15656007	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6043363	PNLDC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15541000-15543800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr20:15541200-15545000	Enhancers	Fetal Stomach	stomach
3	chr20:15541400-15543400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:15541400-15543600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr20:15541400-15543800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:15541600-15542800	Enhancers	Fetal Brain Male	brain
7	chr20:15541600-15543000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:15541600-15543000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:15541600-15543200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr20:15541600-15543200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:15541600-15543200	Enhancers	Fetal Heart	heart
12	chr20:15541600-15543400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr20:15541600-15543400	Enhancers	Brain Angular Gyrus	brain
14	chr20:15541600-15543600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr20:15541600-15543600	Enhancers	Brain Cingulate Gyrus	brain
16	chr20:15541600-15543800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr20:15541600-15544000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr20:15541600-15544800	Enhancers	Brain Substantia Nigra	brain
19	chr20:15541800-15543000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr20:15541800-15543200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr20:15541800-15543200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr20:15541800-15543400	Enhancers	Brain Germinal Matrix	brain
23	chr20:15541800-15543800	Enhancers	Colon Smooth Muscle	Colon
24	chr20:15542000-15543000	Weak transcription	Brain Anterior Caudate	brain
25	chr20:15542000-15543200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr20:15542000-15545200	Weak transcription	Fetal Lung	lung
27	chr20:15542200-15543400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr20:15542400-15542800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr20:15542400-15542800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr20:15542400-15542800	Weak transcription	Brain Hippocampus Middle	brain
31	chr20:15542400-15542800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr20:15542600-15554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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