Variant report

Variant	rs4238539
Chromosome Location	chr15:83464612-83464613
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83463702..83465525-chr15:83476869..83478569,2	MCF-7	breast:
2	chr15:83464584..83467201-chr15:83471409..83474947,3	K562	blood:
3	chr15:83455503..83457802-chr15:83462699..83465751,3	K562	blood:
4	chr15:83464143..83466084-chr15:83470517..83472909,2	K562	blood:
5	chr15:83463198..83465814-chr15:83477864..83479987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186628	Chromatin interaction
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1105867	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12385964	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1256429	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1256434	0.88[JPT][hapmap]
rs1256451	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256452	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1256453	0.88[JPT][hapmap]
rs1256455	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1256456	0.83[EUR][1000 genomes]
rs12905235	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12910279	0.81[EUR][1000 genomes]
rs12914161	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1553883	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17360083	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1877241	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2089844	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2379992	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2379993	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2458017	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2621227	0.88[JPT][hapmap]
rs2621228	0.86[JPT][hapmap]
rs2667383	0.80[EUR][1000 genomes]
rs2667385	0.86[JPT][hapmap]
rs2890313	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2928572	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4779063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779065	0.82[EUR][1000 genomes]
rs7163402	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7169401	0.88[JPT][hapmap]
rs8038679	1.00[CEU][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs8039001	0.81[EUR][1000 genomes]
rs9806543	0.86[JPT][hapmap]

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	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4238539	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs4238539	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83436400-83467800	Weak transcription	Psoas Muscle	Psoas
2	chr15:83440800-83468000	Weak transcription	Right Ventricle	heart
3	chr15:83450400-83477600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:83455600-83467400	Weak transcription	Fetal Heart	heart
5	chr15:83456000-83468200	Weak transcription	Left Ventricle	heart
6	chr15:83456200-83467800	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:83461600-83465400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:83464200-83465000	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:83464200-83465200	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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