Variant report

Variant	rs13019268
Chromosome Location	chr2:46610212-46610213
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	chr2:46609393..46611243-chr2:46614056..46616065,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10191091	0.84[MEX][hapmap]
rs11678465	0.81[ASW][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11678817	0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs11690950	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11690951	0.89[CEU][hapmap];0.81[CHB][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694193	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12467821	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13006131	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13019414	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1530622	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1868093	0.89[YRI][hapmap]
rs1868094	0.89[YRI][hapmap]
rs35145595	0.89[ASN][1000 genomes]
rs3754556	0.91[ASW][hapmap]
rs3768730	0.85[MEX][hapmap]
rs7567582	0.82[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7568285	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7571218	0.93[GIH][hapmap]
rs7583088	0.81[ASW][hapmap];0.82[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7583392	0.81[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7590087	0.82[CEU][hapmap]
rs7594278	0.85[CHB][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7594912	0.85[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7598371	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7606559	0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.81[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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13019268	OXER1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
2	chr2:46574800-46613000	Weak transcription	HSMM	muscle
3	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
4	chr2:46592200-46619800	Weak transcription	K562	blood
5	chr2:46592600-46611200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:46592600-46612600	Strong transcription	NHEK	skin
7	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr2:46593600-46615400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:46594000-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:46594400-46615600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:46594600-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:46594800-46615400	Strong transcription	Liver	Liver
13	chr2:46594800-46615600	Strong transcription	HUVEC	blood vessel
14	chr2:46595000-46616000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:46596000-46612800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:46600600-46612600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:46600800-46614200	Strong transcription	HepG2	liver
18	chr2:46601800-46616400	Genic enhancers	Placenta	Placenta
19	chr2:46602000-46616000	Strong transcription	Pancreas	Pancrea
20	chr2:46602400-46613400	Strong transcription	Fetal Intestine Small	intestine
21	chr2:46603200-46614200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:46604600-46612000	Strong transcription	Aorta	Aorta
23	chr2:46605000-46613000	Strong transcription	A549	lung
24	chr2:46605200-46614200	Weak transcription	Brain Substantia Nigra	brain
25	chr2:46605600-46614800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr2:46606000-46612200	Strong transcription	Colonic Mucosa	Colon
27	chr2:46606000-46615000	Strong transcription	Right Ventricle	heart
28	chr2:46606000-46615400	Strong transcription	Left Ventricle	heart
29	chr2:46606200-46613000	Weak transcription	Right Atrium	heart
30	chr2:46606200-46613400	Strong transcription	Gastric	stomach
31	chr2:46606400-46611200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:46606600-46613000	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:46606600-46614600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:46606800-46613000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:46607000-46612600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:46607000-46612600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:46607000-46613000	Weak transcription	Brain Anterior Caudate	brain
38	chr2:46607000-46613800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:46607000-46617000	Weak transcription	Stomach Mucosa	stomach
40	chr2:46607200-46611200	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:46607200-46611200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr2:46607200-46612000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr2:46607200-46613800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:46607200-46614400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:46607400-46612000	Strong transcription	Ovary	ovary
46	chr2:46607400-46612600	Weak transcription	HMEC	breast
47	chr2:46607400-46612800	Strong transcription	Adipose Nuclei	Adipose
48	chr2:46607600-46610800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:46608000-46610600	Weak transcription	Psoas Muscle	Psoas
50	chr2:46608400-46612000	ZNF genes & repeats	Fetal Stomach	stomach

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