Variant report

Variant	rs13409879
Chromosome Location	chr2:114458022-114458023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114361263..114362251-chr2:114457536..114458288,3	MCF-7	breast:
2	chr2:114361344..114362249-chr2:114457515..114458330,2	MCF-7	breast:
3	chr2:114359257..114359811-chr2:114457510..114458087,2	MCF-7	breast:
4	chr2:114284812..114285348-chr2:114457736..114458446,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10169190	0.84[EUR][1000 genomes]
rs10187723	1.00[ASN][1000 genomes]
rs10188078	1.00[ASN][1000 genomes]
rs10197009	0.87[EUR][1000 genomes]
rs10199515	0.87[EUR][1000 genomes]
rs10206547	1.00[ASN][1000 genomes]
rs1062074	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12329244	0.84[EUR][1000 genomes]
rs12711781	0.91[EUR][1000 genomes]
rs12711787	0.85[EUR][1000 genomes]
rs12998926	1.00[AMR][1000 genomes]
rs13025042	0.84[EUR][1000 genomes]
rs13393247	0.81[EUR][1000 genomes]
rs13395272	0.89[EUR][1000 genomes]
rs13401587	0.85[EUR][1000 genomes]
rs13407986	0.88[EUR][1000 genomes]
rs13408264	0.89[EUR][1000 genomes]
rs13410586	0.84[EUR][1000 genomes]
rs13416738	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13424899	0.87[EUR][1000 genomes]
rs13428433	0.85[EUR][1000 genomes]
rs17048299	0.89[EUR][1000 genomes]
rs17048506	0.87[EUR][1000 genomes]
rs17633451	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28392566	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34004564	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34026450	0.89[EUR][1000 genomes]
rs34451679	0.81[EUR][1000 genomes]
rs34480436	0.84[EUR][1000 genomes]
rs35049717	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35073956	0.89[EUR][1000 genomes]
rs35192494	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35255260	0.87[EUR][1000 genomes]
rs56316177	0.92[AMR][1000 genomes]
rs62170066	0.84[EUR][1000 genomes]
rs7600251	0.85[EUR][1000 genomes]
rs998151	1.00[AMR][1000 genomes];0.91[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	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13409879	ACTR3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114444200-114459200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:114448800-114459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:114451600-114461400	Weak transcription	Esophagus	oesophagus
4	chr2:114451600-114461800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:114451600-114462400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:114452400-114470200	Weak transcription	Primary T cells from cord blood	blood
7	chr2:114452600-114461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:114452600-114469400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:114453000-114470400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:114455000-114470400	Weak transcription	NHEK	skin
11	chr2:114455400-114472200	Weak transcription	HMEC	breast
12	chr2:114455600-114470400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:114455800-114462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:114455800-114470400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:114456400-114458400	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:114456600-114458200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:114456600-114458200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:114456600-114458200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:114456800-114458200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:114456800-114458200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:114456800-114458200	Enhancers	HepG2	liver
22	chr2:114456800-114458400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:114457200-114458200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr2:114457400-114458200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:114457400-114458200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:114457400-114458200	Weak transcription	Spleen	Spleen
27	chr2:114457400-114458400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:114457400-114458400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:114457600-114458200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:114457600-114458200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:114457600-114458200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:114457600-114458200	Flanking Active TSS	GM12878-XiMat	blood
33	chr2:114457600-114458400	Enhancers	Thymus	Thymus
34	chr2:114457800-114458200	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:114457800-114458200	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:114457800-114458200	Enhancers	Dnd41	blood
37	chr2:114457800-114458400	Enhancers	Fetal Thymus	thymus
38	chr2:114457800-114458400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:114458000-114458200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:114458000-114458200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:114458000-114458200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:114458000-114458200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:114458000-114458200	Enhancers	Adipose Nuclei	Adipose
44	chr2:114458000-114458200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr2:114458000-114458200	Flanking Active TSS	K562	blood
46	chr2:114458000-114458400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:114458000-114458400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:114458000-114458400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:114458000-114458400	Enhancers	Placenta	Placenta
50	chr2:114458000-114458400	Enhancers	Left Ventricle	heart

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