Variant report

Variant	rs1499289
Chromosome Location	chr1:224772665-224772666
allele	A/G
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	chr1:224772214-224772790	HepG2	liver:	n/a	n/a
2	MAFK	chr1:224772144-224772746	IMR90	lung:	n/a	chr1:224772372-224772383 chr1:224772212-224772223 chr1:224772211-224772225 chr1:224772649-224772663 chr1:224772212-224772228 chr1:224772650-224772665 chr1:224772650-224772666 chr1:224772213-224772224 chr1:224772651-224772662 chr1:224772372-224772383 chr1:224772212-224772223 chr1:224772619-224772636 chr1:224772370-224772379
3	MAFK	chr1:224772485-224772685	HepG2	liver:	n/a	chr1:224772649-224772663 chr1:224772650-224772665 chr1:224772650-224772666 chr1:224772651-224772662 chr1:224772619-224772636
4	MAFK	chr1:224772493-224772781	HepG2	liver:	n/a	chr1:224772649-224772663 chr1:224772650-224772665 chr1:224772650-224772666 chr1:224772651-224772662 chr1:224772619-224772636

Variant related genes	Relation type
CNIH3	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1036431	0.83[CEU][hapmap]
rs1039265	0.81[CEU][hapmap]
rs10915691	0.83[CEU][hapmap]
rs10915693	0.83[CEU][hapmap]
rs10915695	0.83[CEU][hapmap]
rs10916641	0.85[CHB][hapmap]
rs10916642	0.85[YRI][hapmap]
rs1106233	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060334	0.83[CEU][hapmap]
rs12065840	0.83[CEU][hapmap];0.91[LWK][hapmap]
rs12077707	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12079156	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12088524	0.83[CEU][hapmap]
rs12089565	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12091093	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565092	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337538	0.91[CEU][hapmap]
rs1499291	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499293	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499294	0.83[CHD][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1532557	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16850786	0.83[CEU][hapmap]
rs1985338	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4363402	0.83[CEU][hapmap]
rs58725094	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60500269	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827076	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426147	0.83[CEU][hapmap]
rs6695864	0.92[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73115953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73115958	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415393	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7554310	0.83[CEU][hapmap]
rs883116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs969025	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1499289	PYCR2	cis	cerebellum	SCAN
rs1499289	RAB3GAP2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224753600-224780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224767400-224779600	Weak transcription	HMEC	breast
3	chr1:224767600-224779800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224767800-224780200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224768000-224774400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:224768000-224776400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:224768000-224776600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:224768000-224776800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:224768000-224780400	Weak transcription	Psoas Muscle	Psoas
10	chr1:224768800-224779600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:224770000-224776000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:224770200-224776000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:224771000-224774400	Weak transcription	Aorta	Aorta
14	chr1:224772600-224775400	Weak transcription	Right Atrium	heart

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