Variant report

Variant	rs27245
Chromosome Location	chr5:50142025-50142026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:50139685..50142220-chr5:50145007..50147004,3	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10038842	0.82[EUR][1000 genomes]
rs10039639	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10043477	0.87[EUR][1000 genomes]
rs10070517	0.84[EUR][1000 genomes]
rs10471940	0.82[EUR][1000 genomes]
rs10471956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10755235	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs10940472	0.88[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11739828	0.90[EUR][1000 genomes]
rs11750241	0.88[EUR][1000 genomes]
rs11750771	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12188262	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12188654	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12518710	1.00[JPT][hapmap]
rs12519006	0.97[EUR][1000 genomes]
rs12521579	0.97[EUR][1000 genomes]
rs13153982	0.90[EUR][1000 genomes]
rs13164951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13173734	0.88[EUR][1000 genomes]
rs13359044	0.97[EUR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs152102	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154133	0.97[EUR][1000 genomes]
rs154135	0.96[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154138	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs154141	0.97[EUR][1000 genomes]
rs157970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs169497	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs171555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17195388	0.97[EUR][1000 genomes]
rs182230	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1988613	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2354526	0.82[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2548582	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2548583	0.96[EUR][1000 genomes]
rs256340	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs256341	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs26062	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs26065	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs26066	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs26068	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs26069	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs26071	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs27156	0.97[EUR][1000 genomes]
rs27244	0.97[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs27254	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs27264	0.83[EUR][1000 genomes]
rs27357	0.99[EUR][1000 genomes]
rs27465	0.96[EUR][1000 genomes]
rs27467	1.00[CEU][hapmap]
rs27468	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs27469	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs27574	0.97[EUR][1000 genomes]
rs27609	0.94[EUR][1000 genomes]
rs27627	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs27725	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28085	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs282549	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs282550	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs282551	0.96[EUR][1000 genomes]
rs282552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs282553	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs282557	0.88[EUR][1000 genomes]
rs282559	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs282561	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs32377	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs32378	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs32404	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs32425	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3763367	0.83[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs39949	0.87[EUR][1000 genomes]
rs4029420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs41502	0.94[EUR][1000 genomes]
rs42284	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4865628	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4865974	1.00[JPT][hapmap]
rs4866001	1.00[JPT][hapmap]
rs57079776	0.81[EUR][1000 genomes]
rs578198	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59900589	0.81[EUR][1000 genomes]
rs62366937	0.86[EUR][1000 genomes]
rs6450301	0.82[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6869356	0.87[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs6886872	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs6890519	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6890869	1.00[CEU][hapmap]
rs7449019	0.84[EUR][1000 genomes]
rs7711839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7723361	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7734389	0.82[EUR][1000 genomes]
rs895801	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
3	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27245	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs27245	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50108200-50142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:50119200-50144200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:50124200-50145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:50125200-50142800	Weak transcription	HMEC	breast
7	chr5:50125200-50143200	Weak transcription	Left Ventricle	heart
8	chr5:50125400-50149200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:50125800-50143200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:50126400-50143200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:50129200-50148400	Weak transcription	GM12878-XiMat	blood
12	chr5:50132600-50148400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:50132800-50142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:50133400-50150000	Weak transcription	Adipose Nuclei	Adipose
15	chr5:50138600-50144400	Weak transcription	Liver	Liver
16	chr5:50139200-50143400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:50139800-50142600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:50140000-50142800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:50140000-50142800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:50140000-50143400	Weak transcription	Primary T cells from cord blood	blood
21	chr5:50140000-50143400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:50140000-50144400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:50140200-50148600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:50140400-50142600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:50140600-50148200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr5:50140800-50143200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:50140800-50143200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:50141400-50152400	Weak transcription	Dnd41	blood
29	chr5:50141600-50147600	Weak transcription	Primary B cells from cord blood	blood
30	chr5:50141600-50152800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:50141800-50143800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:50141800-50147800	Weak transcription	Monocytes-CD14+_RO01746	blood

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