Variant report

Variant	rs13159553
Chromosome Location	chr5:49886600-49886601
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	chr5:49735466..49737250-chr5:49884402..49886909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170571	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13153852	0.89[EUR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes]
rs13157952	0.93[EUR][1000 genomes]
rs13162663	0.91[EUR][1000 genomes]
rs13167408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169200	0.98[EUR][1000 genomes]
rs13171248	0.93[EUR][1000 genomes]
rs13172426	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13172836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes]
rs13180485	0.89[EUR][1000 genomes]
rs13180506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13183686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968637	0.93[EUR][1000 genomes]
rs1968639	0.89[AFR][1000 genomes]
rs2354531	0.93[EUR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes]
rs34443769	0.89[EUR][1000 genomes]
rs35210389	0.91[EUR][1000 genomes]
rs35292338	0.98[EUR][1000 genomes]
rs35434227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35596019	0.98[EUR][1000 genomes]
rs36187734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892149	0.91[EUR][1000 genomes]
rs71615974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71631479	0.89[EUR][1000 genomes]
rs71631481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7708492	0.93[AFR][1000 genomes]
rs7723395	0.93[EUR][1000 genomes]
rs7730188	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv10697	chr5:49885405-49887075	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv14399	chr5:49885912-49934455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13159553	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49876800-49891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:49884800-49886800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:49884800-49888200	Weak transcription	HMEC	breast
4	chr5:49885600-49887000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:49885600-49887400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:49885600-49888600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:49885600-49888800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:49885600-49889000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:49885600-49890600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:49885600-49890600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr5:49885600-49891400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:49885600-49891400	Enhancers	Dnd41	blood
13	chr5:49885600-49891800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:49885800-49891400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr5:49885800-49891800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr5:49886200-49887400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:49886200-49887400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr5:49886200-49887600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:49886200-49890200	Enhancers	Primary T cells from cord blood	blood
20	chr5:49886200-49890200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:49886200-49890400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:49886200-49890600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:49886200-49891000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:49886200-49891400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:49886400-49886600	Enhancers	NHEK	skin
26	chr5:49886400-49887000	Enhancers	Primary hematopoietic stem cells	blood
27	chr5:49886400-49887200	Enhancers	Osteobl	bone
28	chr5:49886400-49887400	Enhancers	Hela-S3	cervix
29	chr5:49886400-49888600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr5:49886400-49890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:49886600-49886800	Enhancers	NHDF-Ad	bronchial
32	chr5:49886600-49887000	Weak transcription	NHEK	skin

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