Variant report

Variant	rs803688
Chromosome Location	chr15:83216793-83216794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83215974..83218475-chr15:83222102..83225173,3	MCF-7	breast:
2	chr15:83216717..83218665-chr15:83313410..83315739,2	K562	blood:
3	chr15:83216641..83218294-chr15:83221044..83223302,2	K562	blood:
4	chr15:83215297..83217273-chr15:83218215..83220655,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260836	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10400906	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10468217	0.92[ASN][1000 genomes]
rs10906984	0.83[ASN][1000 genomes]
rs1145172	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145173	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631963	0.83[EUR][1000 genomes]
rs11633829	0.85[ASN][1000 genomes]
rs11637433	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855735	0.84[ASN][1000 genomes]
rs12148332	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12438312	0.83[ASN][1000 genomes]
rs12442686	0.81[ASN][1000 genomes]
rs1259180	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1259182	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1259183	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1267657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267658	0.97[ASN][1000 genomes]
rs1267659	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1269134	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12916980	0.87[ASN][1000 genomes]
rs1313492	0.90[ASN][1000 genomes]
rs1313493	0.90[ASN][1000 genomes]
rs1367841	0.87[ASN][1000 genomes]
rs1594511	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158390	0.86[ASN][1000 genomes]
rs1864699	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099259	0.87[ASN][1000 genomes]
rs2278355	0.83[ASN][1000 genomes]
rs2567635	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2567636	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2678445	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678448	0.90[ASN][1000 genomes]
rs28374463	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28415133	0.90[ASN][1000 genomes]
rs28493687	0.88[AFR][1000 genomes]
rs2870965	0.83[ASN][1000 genomes]
rs2870966	0.86[ASN][1000 genomes]
rs2871011	0.88[AFR][1000 genomes]
rs28808991	0.92[ASN][1000 genomes]
rs34186444	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35934048	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36109438	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3970696	0.90[ASN][1000 genomes]
rs4778686	0.87[ASN][1000 genomes]
rs4779032	0.94[ASN][1000 genomes]
rs4779041	0.87[ASN][1000 genomes]
rs4779044	0.86[ASN][1000 genomes]
rs4779050	0.83[ASN][1000 genomes]
rs55924160	0.86[ASN][1000 genomes]
rs57181760	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6603033	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698500	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165125	0.84[ASN][1000 genomes]
rs7167880	0.86[ASN][1000 genomes]
rs7171180	0.87[ASN][1000 genomes]
rs7178350	0.83[ASN][1000 genomes]
rs7182403	0.86[ASN][1000 genomes]
rs7183881	0.86[ASN][1000 genomes]
rs7494860	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7496954	0.86[ASN][1000 genomes]
rs783520	0.85[ASN][1000 genomes]
rs783521	0.86[ASN][1000 genomes]
rs783522	0.86[ASN][1000 genomes]
rs783523	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs783525	0.86[ASN][1000 genomes]
rs783526	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783527	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783529	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783530	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783531	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs783532	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783533	0.91[ASN][1000 genomes]
rs783534	0.91[ASN][1000 genomes]
rs783535	0.88[ASN][1000 genomes]
rs783536	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783537	0.90[ASN][1000 genomes]
rs783539	0.90[ASN][1000 genomes]
rs783540	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783543	0.88[ASN][1000 genomes]
rs783545	0.94[ASN][1000 genomes]
rs803687	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs803747	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040293	0.83[ASN][1000 genomes]
rs8043401	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv428645	chr15:83069951-83227151	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv10828	chr15:83096440-83219640	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs803688	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs803688	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs803688	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs803688	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83213000-83217200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:83213200-83217400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:83213200-83220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:83213600-83218600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:83213800-83217400	Weak transcription	Aorta	Aorta
6	chr15:83214000-83217200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:83214000-83217200	Weak transcription	Fetal Lung	lung
8	chr15:83214000-83224800	Strong transcription	Stomach Smooth Muscle	stomach
9	chr15:83214200-83217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:83214200-83222600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:83214600-83226800	Weak transcription	Gastric	stomach
12	chr15:83215200-83217400	Weak transcription	Fetal Stomach	stomach
13	chr15:83215600-83221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:83215800-83217200	Weak transcription	K562	blood
15	chr15:83216000-83216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:83216000-83217200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:83216000-83218200	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:83216000-83220600	Weak transcription	HSMMtube	muscle
19	chr15:83216200-83217000	Weak transcription	Brain Angular Gyrus	brain
20	chr15:83216200-83217000	Weak transcription	Brain Anterior Caudate	brain
21	chr15:83216200-83217000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:83216200-83217000	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:83216200-83217000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:83216200-83217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:83216200-83217000	Weak transcription	Brain Substantia Nigra	brain
26	chr15:83216200-83222400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:83216600-83221000	Weak transcription	Ovary	ovary

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