Variant report

Variant	rs13163802
Chromosome Location	chr5:50140765-50140766
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	chr5:50139685..50142220-chr5:50145007..50147004,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10052372	0.92[EUR][1000 genomes]
rs11950506	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11952107	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11955934	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11959326	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13156735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13157079	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13159239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13161225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13163470	0.96[EUR][1000 genomes]
rs13166819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13169153	0.96[EUR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13181031	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13181117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13183910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13186653	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13189183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13190144	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16886309	0.96[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34264957	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34414061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34677483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34758774	0.87[EUR][1000 genomes]
rs34827507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34855203	0.83[EUR][1000 genomes]
rs35128589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35347195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35473824	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41270305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6880398	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6883701	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6888271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6888315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71615978	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71615981	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71615983	0.96[EUR][1000 genomes]
rs71615984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71615990	1.00[EUR][1000 genomes]
rs71615991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7717073	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7726225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7733931	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13163802	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 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	chr5:50109400-50141800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr5:50110000-50141800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:50111000-50140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:50111200-50141600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:50119200-50144200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:50124200-50145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:50124400-50141400	Weak transcription	Fetal Intestine Large	intestine
11	chr5:50124400-50141600	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:50125200-50142800	Weak transcription	HMEC	breast
13	chr5:50125200-50143200	Weak transcription	Left Ventricle	heart
14	chr5:50125400-50149200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:50125800-50143200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:50126400-50143200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:50129200-50148400	Weak transcription	GM12878-XiMat	blood
18	chr5:50130600-50141400	Strong transcription	Dnd41	blood
19	chr5:50130800-50141400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:50132600-50141200	Weak transcription	Aorta	Aorta
21	chr5:50132600-50148400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:50132800-50142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:50133200-50140800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr5:50133400-50150000	Weak transcription	Adipose Nuclei	Adipose
25	chr5:50137000-50141600	Strong transcription	Primary B cells from cord blood	blood
26	chr5:50137800-50140800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:50138600-50141400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:50138600-50144400	Weak transcription	Liver	Liver
29	chr5:50138800-50141400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:50139200-50143400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:50139600-50141000	Weak transcription	Ovary	ovary
32	chr5:50139800-50141400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:50139800-50142600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:50140000-50141400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr5:50140000-50141600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:50140000-50141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:50140000-50141800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:50140000-50142000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:50140000-50142800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:50140000-50142800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:50140000-50143400	Weak transcription	Primary T cells from cord blood	blood
42	chr5:50140000-50143400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:50140000-50144400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:50140200-50142000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:50140200-50148600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:50140400-50142600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:50140600-50148200	Weak transcription	Primary B cells from peripheral blood	blood

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