Variant report

Variant	rs27934
Chromosome Location	chr5:50118959-50118960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:50115536..50118140-chr5:50118384..50120343,2	MCF-7	breast:
2	chr5:50111976..50114823-chr5:50117408..50119035,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10471414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10512906	0.85[JPT][hapmap]
rs10737958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11747930	0.85[JPT][hapmap]
rs11954386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12055210	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12153387	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12186752	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12653772	0.85[JPT][hapmap]
rs13162945	0.85[JPT][hapmap]
rs13180000	0.85[JPT][hapmap]
rs13186089	0.85[JPT][hapmap]
rs1375128	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs152001	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154136	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs166863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1993955	0.85[JPT][hapmap]
rs204915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354533	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2404958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2463796	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2463797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2594708	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27243	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27598	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27964	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs282548	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282555	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs282560	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32396	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36077571	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3806887	0.85[JPT][hapmap]
rs4548483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55932149	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56670602	0.86[EUR][1000 genomes]
rs61401688	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62366941	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6450384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6450391	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66912405	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7717033	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs27934	PARP8	cis	Adipose Subcutaneous	GTEx
rs27934	PARP8	cis	Esophagus Muscularis	GTEx
rs27934	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:50064000-50126800	Weak transcription	Osteobl	bone
3	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
4	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
7	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
8	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
9	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
10	chr5:50091200-50133600	Weak transcription	Lung	lung
11	chr5:50091200-50136000	Weak transcription	Gastric	stomach
12	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
13	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:50094000-50123800	Weak transcription	HMEC	breast
16	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
17	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:50099400-50123800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:50100200-50139400	Weak transcription	Ovary	ovary
20	chr5:50100400-50123800	Weak transcription	Left Ventricle	heart
21	chr5:50104600-50129400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:50104600-50136200	Weak transcription	NHEK	skin
23	chr5:50104800-50123600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:50108000-50135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:50108200-50142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:50109400-50124000	Weak transcription	Fetal Intestine Large	intestine
27	chr5:50109400-50141800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:50109600-50129000	Strong transcription	Dnd41	blood
29	chr5:50109800-50134400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:50109800-50136400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:50110000-50141800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr5:50110400-50128000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:50110400-50133400	Strong transcription	Primary B cells from cord blood	blood
34	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:50110600-50134600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:50110800-50132000	Weak transcription	Brain Substantia Nigra	brain
38	chr5:50110800-50133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:50110800-50140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:50111000-50140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:50111200-50121000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:50111200-50141600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:50111400-50124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:50111400-50127000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:50111800-50121800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:50112000-50119000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:50112000-50119400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:50112200-50120600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:50112400-50125200	Weak transcription	Brain Anterior Caudate	brain
50	chr5:50113000-50139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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