Variant report

Variant	rs17259572
Chromosome Location	chr4:106961234-106961235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106954975..106957193-chr4:106960681..106963190,2	MCF-7	breast:

Extended variants
information (count: 167 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs10002288	1.00[ASN][1000 genomes]
rs10016884	0.95[CEU][hapmap]
rs10025052	1.00[ASN][1000 genomes]
rs10030019	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10084928	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10516532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516533	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097912	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs11097914	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097916	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097925	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942153	1.00[ASN][1000 genomes]
rs12499891	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12502764	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12503753	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504721	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505689	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12506062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506658	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12507867	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507874	0.89[ASN][1000 genomes]
rs12508432	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12508552	0.99[ASN][1000 genomes]
rs12509366	0.99[ASN][1000 genomes]
rs12509640	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12509865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12510058	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510966	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12511305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512683	0.99[ASN][1000 genomes]
rs12512877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12512903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12512966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12513317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639678	0.97[ASN][1000 genomes]
rs12639869	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12641015	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12641037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642059	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12642227	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12642900	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12643397	0.99[ASN][1000 genomes]
rs12644259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12645255	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12645698	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645743	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12646263	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646485	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647078	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649709	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651360	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036613	0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17273093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17273445	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17274017	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17333287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28391259	0.99[ASN][1000 genomes]
rs28507027	0.99[ASN][1000 genomes]
rs28765420	0.96[ASN][1000 genomes]
rs28787305	0.99[ASN][1000 genomes]
rs28814088	0.92[ASN][1000 genomes]
rs28822186	0.99[ASN][1000 genomes]
rs28866820	0.99[ASN][1000 genomes]
rs28868894	0.99[ASN][1000 genomes]
rs28875879	0.99[ASN][1000 genomes]
rs28897193	0.99[ASN][1000 genomes]
rs34193646	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34899289	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34961213	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35518913	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775090	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4323181	0.99[ASN][1000 genomes]
rs4337798	0.99[ASN][1000 genomes]
rs4337799	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4339284	0.99[ASN][1000 genomes]
rs4422480	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4429790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4458525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4466113	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4521418	0.98[ASN][1000 genomes]
rs55633564	0.99[ASN][1000 genomes]
rs55634475	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55833794	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56009469	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56135499	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56222430	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56231393	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56260521	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56329826	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56333662	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56341229	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56775039	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57246774	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59784613	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60538413	0.90[ASN][1000 genomes]
rs61544154	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62321365	0.96[ASN][1000 genomes]
rs6533240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533243	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6810877	0.96[ASN][1000 genomes]
rs6815014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816614	0.99[ASN][1000 genomes]
rs6818197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6818626	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822692	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823347	1.00[ASN][1000 genomes]
rs6824682	0.99[ASN][1000 genomes]
rs6828362	0.99[ASN][1000 genomes]
rs6829795	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs6835216	0.83[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs6842919	0.99[ASN][1000 genomes]
rs6843331	0.99[ASN][1000 genomes]
rs6843870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6844324	0.99[ASN][1000 genomes]
rs6846579	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs72489522	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72677306	0.99[ASN][1000 genomes]
rs72876575	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72893620	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340989	0.91[ASN][1000 genomes]
rs7655054	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657962	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7657975	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7658011	1.00[ASN][1000 genomes]
rs7658701	0.99[ASN][1000 genomes]
rs7661499	0.94[ASN][1000 genomes]
rs7661565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7662219	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7662291	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7662395	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7662592	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7662806	0.99[ASN][1000 genomes]
rs7662836	0.99[ASN][1000 genomes]
rs7664032	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664188	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7665946	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667719	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7668477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7669087	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7669212	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7671145	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7673949	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674381	0.88[ASN][1000 genomes]
rs7674466	0.92[ASN][1000 genomes]
rs7674931	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675728	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677248	1.00[ASN][1000 genomes]
rs7678229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678847	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7681257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7688411	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692069	0.96[ASN][1000 genomes]
rs7698386	0.97[ASN][1000 genomes]
rs7699768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9684658	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9685018	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685464	0.99[ASN][1000 genomes]
rs9991091	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17259572	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs17259572	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs17259572	MGC16169	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106955000-106969600	Weak transcription	NHLF	lung
2	chr4:106955200-106966600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:106956000-106961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:106956000-106969800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:106956200-106967200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:106956200-106967400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:106956200-106968200	Weak transcription	Fetal Stomach	stomach
8	chr4:106956200-106969600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:106956200-106970000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:106956400-106966600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:106956600-106961600	Weak transcription	Psoas Muscle	Psoas
12	chr4:106956600-106969200	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:106956800-106970800	Weak transcription	HSMMtube	muscle
14	chr4:106958000-106966600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:106958400-106969200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:106958400-106969400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:106959200-106969000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:106959200-106969800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:106959600-106969200	Weak transcription	Pancreas	Pancrea
20	chr4:106959600-106969600	Weak transcription	Fetal Kidney	kidney
21	chr4:106959600-106983400	Weak transcription	HepG2	liver
22	chr4:106960600-106965000	Enhancers	Fetal Heart	heart
23	chr4:106960600-106969400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:106961200-106961400	Weak transcription	NHDF-Ad	bronchial
25	chr4:106961200-106966600	Weak transcription	Fetal Lung	lung

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