Variant report

Variant	rs2243461
Chromosome Location	chr13:48841518-48841519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48839695..48841819-chr13:48848879..48850902,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10219833	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12100135	0.95[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12430215	0.90[CEU][hapmap]
rs12871662	0.84[EUR][1000 genomes]
rs12871740	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12875750	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1573601	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs1886795	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1925744	0.86[EUR][1000 genomes]
rs1925745	0.86[EUR][1000 genomes]
rs1951775	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs1981434	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1981435	0.83[EUR][1000 genomes]
rs198563	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs198584	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs198590	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs198604	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs198607	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs198612	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs198619	1.00[CEU][hapmap]
rs2243626	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251813	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253520	0.91[EUR][1000 genomes]
rs2254423	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2406933	0.91[EUR][1000 genomes]
rs34217484	0.91[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs3809328	0.95[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818455	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs399413	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs4151450	1.00[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs4594153	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4600372	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520342	0.90[CEU][hapmap]
rs61973349	0.84[EUR][1000 genomes]
rs7322987	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7358982	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7984554	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984795	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7999447	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8001315	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316367	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9316369	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9526465	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526466	0.86[EUR][1000 genomes]
rs9526470	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526475	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs9534996	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534998	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9535000	0.86[EUR][1000 genomes]
rs9535002	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535003	0.86[EUR][1000 genomes]
rs9535006	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9535007	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535009	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9535011	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535016	0.81[EUR][1000 genomes]
rs9535032	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs9562819	0.85[CEU][hapmap]
rs9568026	0.89[EUR][1000 genomes]
rs9568027	0.84[EUR][1000 genomes]
rs9568028	0.84[EUR][1000 genomes]
rs9568029	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2243461	LPAR6	cis	parietal	SCAN
rs2243461	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs2243461	DLEU1	cis	parietal	SCAN
rs2243461	ATAD2	trans	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48808400-48843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48811200-48843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:48825400-48844400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr13:48826800-48842000	Weak transcription	K562	blood
5	chr13:48827600-48843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:48827800-48843800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:48828600-48845800	Weak transcription	Stomach Mucosa	stomach
8	chr13:48829800-48843400	Weak transcription	Spleen	Spleen
9	chr13:48832800-48845200	Weak transcription	Fetal Intestine Small	intestine
10	chr13:48833000-48843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:48833600-48843600	Weak transcription	Pancreas	Pancrea
12	chr13:48833600-48844400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:48833800-48851600	Weak transcription	Fetal Heart	heart
14	chr13:48835800-48849400	Weak transcription	NHLF	lung
15	chr13:48837800-48848000	Weak transcription	A549	lung
16	chr13:48837800-48848600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:48837800-48848600	Weak transcription	Fetal Brain Female	brain
18	chr13:48837800-48853000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:48837800-48856400	Weak transcription	Colon Smooth Muscle	Colon
20	chr13:48838000-48842600	Weak transcription	Thymus	Thymus
21	chr13:48838000-48843000	Weak transcription	Esophagus	oesophagus
22	chr13:48838000-48843200	Weak transcription	Brain Angular Gyrus	brain
23	chr13:48838000-48843400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:48838000-48845200	Weak transcription	Brain Germinal Matrix	brain
25	chr13:48838000-48845600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:48838000-48845600	Weak transcription	HMEC	breast
27	chr13:48838000-48847000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:48838000-48847800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr13:48838000-48847800	Weak transcription	Psoas Muscle	Psoas
30	chr13:48838000-48849600	Weak transcription	Right Ventricle	heart
31	chr13:48838000-48850000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:48838000-48850000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:48838000-48852800	Weak transcription	HUVEC	blood vessel
34	chr13:48838200-48842000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr13:48838200-48845400	Weak transcription	Fetal Intestine Large	intestine
36	chr13:48838200-48849600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:48838400-48845200	Weak transcription	Osteobl	bone
38	chr13:48838400-48846600	Weak transcription	NHDF-Ad	bronchial
39	chr13:48838400-48847000	Weak transcription	Brain Substantia Nigra	brain
40	chr13:48838600-48842400	Weak transcription	HepG2	liver
41	chr13:48838600-48843800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:48839200-48845200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr13:48839200-48846200	Weak transcription	Brain Hippocampus Middle	brain
44	chr13:48839800-48842800	Weak transcription	Fetal Lung	lung
45	chr13:48839800-48843000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:48839800-48843200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:48839800-48843200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:48839800-48843200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:48839800-48843400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr13:48839800-48843400	Weak transcription	Gastric	stomach

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