Variant report

Variant	rs1562361
Chromosome Location	chr2:72905438-72905439
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	chr2:72904382..72907029-chr2:72919984..72921758,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10180259	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496185	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs10496187	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs11126369	0.86[YRI][hapmap]
rs11126378	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11126382	0.88[AFR][1000 genomes]
rs11126386	0.88[AFR][1000 genomes]
rs11689339	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689707	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs11884266	0.96[YRI][hapmap];0.87[AMR][1000 genomes]
rs11892598	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12614041	0.81[AFR][1000 genomes]
rs12615875	0.81[AFR][1000 genomes]
rs12619068	0.88[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs12619565	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs17008241	0.85[CEU][hapmap]
rs17008293	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs17008315	0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17008360	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008369	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876488	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2068410	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4597553	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs4852292	0.82[YRI][hapmap]
rs4852896	0.80[AFR][1000 genomes]
rs55642420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058174	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57192957	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58890506	0.89[AFR][1000 genomes]
rs59216875	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60284189	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60314340	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584321	0.80[AFR][1000 genomes]
rs61619102	0.89[AFR][1000 genomes]
rs61736520	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6546777	0.85[YRI][hapmap]
rs66469454	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509842	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66794803	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713712	0.85[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6716335	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6720889	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs6736649	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739768	0.85[CEU][hapmap]
rs6740390	0.84[CEU][hapmap]
rs6749495	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6754072	1.00[ASN][1000 genomes]
rs6756070	0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs6761253	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs67926386	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67927720	0.85[AFR][1000 genomes]
rs72846963	0.83[EUR][1000 genomes]
rs7565198	0.85[YRI][hapmap]
rs7586886	0.83[AFR][1000 genomes]
rs7591025	0.85[YRI][hapmap]
rs7593084	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7604083	0.85[CEU][hapmap]
rs7604402	0.85[YRI][hapmap]
rs7604818	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7607226	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs764766	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

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	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1562361	CD207	cis	cerebellum	SCAN
rs1562361	TGFA	cis	cerebellum	SCAN
rs1562361	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72896800-72943000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:72897000-72912600	Weak transcription	NHLF	lung
3	chr2:72897800-72909800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:72900200-72911800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:72901600-72905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:72901600-72919200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:72902600-72913200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:72902600-72921200	Weak transcription	Adipose Nuclei	Adipose
9	chr2:72902800-72909200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:72903000-72909400	Weak transcription	Gastric	stomach
11	chr2:72903000-72910600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:72903400-72905600	Enhancers	Fetal Stomach	stomach
13	chr2:72903400-72905800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:72903600-72906000	Enhancers	Fetal Kidney	kidney
15	chr2:72903600-72937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:72903800-72921800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:72903800-72922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:72904200-72905800	Enhancers	Ovary	ovary
19	chr2:72904200-72916400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:72904200-72916600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:72904400-72913000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:72904400-72916400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:72904400-72922000	Weak transcription	NHDF-Ad	bronchial
24	chr2:72904400-72939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:72904600-72905600	Enhancers	HSMMtube	muscle
26	chr2:72904600-72905800	Enhancers	Fetal Lung	lung
27	chr2:72904800-72905600	Enhancers	A549	lung
28	chr2:72904800-72916800	Weak transcription	NHEK	skin
29	chr2:72905000-72908400	Weak transcription	HepG2	liver
30	chr2:72905200-72905600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:72905200-72905600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:72905200-72908400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:72905400-72905600	Enhancers	Esophagus	oesophagus
34	chr2:72905400-72905600	Enhancers	Fetal Heart	heart
35	chr2:72905400-72905600	Enhancers	Placenta	Placenta
36	chr2:72905400-72905600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:72905400-72905800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:72905400-72905800	Enhancers	Brain Angular Gyrus	brain
39	chr2:72905400-72905800	Enhancers	Fetal Brain Male	brain
40	chr2:72905400-72905800	Enhancers	Fetal Muscle Trunk	muscle
41	chr2:72905400-72905800	Enhancers	Fetal Muscle Leg	muscle
42	chr2:72905400-72905800	Enhancers	Left Ventricle	heart
43	chr2:72905400-72905800	Enhancers	Pancreas	Pancrea
44	chr2:72905400-72905800	Enhancers	Psoas Muscle	Psoas
45	chr2:72905400-72905800	Enhancers	Right Ventricle	heart
46	chr2:72905400-72905800	Enhancers	Small Intestine	intestine
47	chr2:72905400-72905800	Enhancers	HSMM	muscle
48	chr2:72905400-72906000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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