Variant report

Variant	rs34827507
Chromosome Location	chr5:50061048-50061049
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	chr5:50059065..50062020-chr5:50078028..50080848,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10052372	0.96[EUR][1000 genomes]
rs11950506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952107	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11955934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11959326	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13153852	0.89[AMR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13156735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13157079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13159239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13161225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13163470	1.00[EUR][1000 genomes]
rs13163802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13166819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13169153	1.00[EUR][1000 genomes]
rs13169200	1.00[AMR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180485	0.89[AMR][1000 genomes]
rs13181031	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13181117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13183910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13186653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13189183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13190144	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16886309	1.00[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34264957	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34414061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34443769	1.00[AMR][1000 genomes]
rs34677483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34758774	0.90[EUR][1000 genomes]
rs34855203	0.87[EUR][1000 genomes]
rs35128589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35292338	1.00[AMR][1000 genomes]
rs35347195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35473824	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35596019	1.00[AMR][1000 genomes]
rs41270305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6880398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6883701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892149	0.89[AMR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes]
rs71615978	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615981	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71615983	1.00[EUR][1000 genomes]
rs71615984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615990	0.96[EUR][1000 genomes]
rs71615991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71631479	1.00[AMR][1000 genomes]
rs7717073	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7726225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7730188	1.00[AMR][1000 genomes]
rs7733931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	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
10	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv462164	chr5:50017724-50063035	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv598115	chr5:50017724-50063035	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34827507	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50039200-50067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:50040000-50069200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:50041400-50068800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:50041800-50069200	Weak transcription	Adipose Nuclei	Adipose
5	chr5:50041800-50070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
7	chr5:50046600-50068600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:50047400-50069000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:50047800-50069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:50051200-50084600	Weak transcription	NHEK	skin
11	chr5:50051600-50068800	Weak transcription	Fetal Lung	lung
12	chr5:50052000-50078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:50052200-50067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:50052600-50069200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:50054400-50069400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:50054800-50062400	Weak transcription	HMEC	breast
18	chr5:50055800-50065200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:50056200-50061200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:50056200-50062400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:50056400-50061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:50056600-50062800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:50056600-50063000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:50056600-50070000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:50056800-50064200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:50056800-50067800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:50057200-50067400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:50057400-50061800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:50057400-50064000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr5:50057600-50065000	Strong transcription	Primary B cells from cord blood	blood
32	chr5:50057800-50061400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:50057800-50063800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:50057800-50084600	Weak transcription	Ovary	ovary
35	chr5:50057800-50090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:50058000-50063200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:50058000-50070000	Weak transcription	Lung	lung
38	chr5:50058000-50090600	Weak transcription	Aorta	Aorta
39	chr5:50058200-50070800	Weak transcription	Spleen	Spleen
40	chr5:50058200-50075200	Weak transcription	Gastric	stomach
41	chr5:50058200-50084600	Weak transcription	Fetal Thymus	thymus
42	chr5:50058200-50092400	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:50058400-50068800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:50058400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:50058800-50068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:50059000-50061400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:50059000-50062400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:50059800-50062000	Weak transcription	HSMMtube	muscle
49	chr5:50060000-50062600	Weak transcription	Fetal Heart	heart
50	chr5:50060000-50066200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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