Variant report

Variant	rs1145173
Chromosome Location	chr15:83223425-83223426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83222033..83224471-chr15:83230402..83232707,2	MCF-7	breast:
2	chr15:83222088..83224291-chr15:83225999..83227759,2	MCF-7	breast:
3	chr15:83223012..83224656-chr15:83233813..83235833,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400906	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10468217	0.92[ASN][1000 genomes]
rs10906984	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs1145172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11633829	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11635624	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs11637433	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855735	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs12148332	0.83[AFR][1000 genomes];0.85[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	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1259182	0.86[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1267657	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267658	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1267659	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1269134	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12916980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1313492	0.90[ASN][1000 genomes]
rs1313493	0.90[ASN][1000 genomes]
rs1367841	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1594511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158390	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1864699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099259	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2278355	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2567635	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2567636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2678445	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678448	0.90[ASN][1000 genomes]
rs28374463	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28415133	0.90[ASN][1000 genomes]
rs2870965	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2870966	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2871011	0.93[LWK][hapmap];0.85[MKK][hapmap]
rs28808991	0.92[ASN][1000 genomes]
rs34186444	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35934048	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36109438	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3970696	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4778686	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs4779032	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4779039	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs4779041	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4779050	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs55924160	0.86[ASN][1000 genomes]
rs57181760	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6603033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698500	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165125	0.84[ASN][1000 genomes]
rs7167880	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs7171180	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7178350	0.83[ASN][1000 genomes]
rs7181761	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap]
rs7182403	0.86[ASN][1000 genomes]
rs7183881	0.86[ASN][1000 genomes]
rs7494860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7496954	0.86[ASN][1000 genomes]
rs783520	0.85[ASN][1000 genomes]
rs783521	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs783522	0.86[ASN][1000 genomes]
rs783523	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs783525	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs783526	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs783527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783530	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783531	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs783532	0.86[AFR][1000 genomes];0.89[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	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs783540	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs783545	0.94[ASN][1000 genomes]
rs803686	0.81[GIH][hapmap]
rs803687	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs803688	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs803747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040293	0.83[ASN][1000 genomes]
rs8043401	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs9652567	0.90[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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
rs1145173	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs1145173	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs1145173	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs1145173	RP11-152F13.8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83214000-83224800	Strong transcription	Stomach Smooth Muscle	stomach
2	chr15:83214600-83226800	Weak transcription	Gastric	stomach
3	chr15:83216800-83235000	Weak transcription	NHLF	lung
4	chr15:83218200-83224800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:83218600-83224800	Weak transcription	Fetal Lung	lung
6	chr15:83219000-83239400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:83219800-83225800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:83219800-83239800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:83220600-83223800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:83221600-83223800	Genic enhancers	Brain Angular Gyrus	brain
11	chr15:83222000-83223800	Genic enhancers	Brain Inferior Temporal Lobe	brain
12	chr15:83222000-83224000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:83222000-83224600	Genic enhancers	Brain Cingulate Gyrus	brain
14	chr15:83222000-83235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:83222000-83239200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:83222200-83223800	Enhancers	Brain Hippocampus Middle	brain
17	chr15:83222200-83224200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:83222200-83227200	Weak transcription	K562	blood
19	chr15:83222200-83237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:83222400-83223600	Enhancers	HMEC	breast
21	chr15:83222400-83223800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:83222400-83224000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:83222400-83224200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:83222400-83224200	Enhancers	NHDF-Ad	bronchial
25	chr15:83222600-83223800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:83222600-83223800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr15:83222600-83223800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:83222600-83223800	Enhancers	Brain Substantia Nigra	brain
29	chr15:83222600-83223800	Enhancers	HSMMtube	muscle
30	chr15:83222600-83223800	Enhancers	NHEK	skin
31	chr15:83222600-83224000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:83222600-83224200	Enhancers	Osteobl	bone
33	chr15:83222600-83225400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:83222600-83239400	Weak transcription	Fetal Stomach	stomach
35	chr15:83222600-83239600	Weak transcription	Ovary	ovary
36	chr15:83222600-83239600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:83222800-83224000	Enhancers	Brain Anterior Caudate	brain
38	chr15:83222800-83240600	Weak transcription	Aorta	Aorta
39	chr15:83223000-83223600	Weak transcription	Psoas Muscle	Psoas
40	chr15:83223200-83223800	Enhancers	HSMM	muscle
41	chr15:83223200-83224000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:83223400-83230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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