Variant report

Variant	rs1559599
Chromosome Location	chr6:143658343-143658344
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	chr6:143657963..143658930-chr6:143748298..143749116,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11751030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11751506	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11752523	0.83[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs11753012	0.83[CEU][hapmap]
rs11753048	0.83[CEU][hapmap]
rs11753058	0.87[CEU][hapmap]
rs11754065	0.83[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs11754096	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs11755477	0.82[CEU][hapmap]
rs11757293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11758932	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1364651	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2161972	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2303386	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2328478	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28502112	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35362528	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4895606	0.85[GIH][hapmap]
rs4895607	0.82[CEU][hapmap]
rs4896632	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs4896633	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs4896634	0.83[TSI][hapmap]
rs4896635	0.82[CEU][hapmap]
rs4896636	0.82[CEU][hapmap]
rs4896637	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs4896639	0.82[CEU][hapmap]
rs4896650	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6924104	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6937858	0.88[CEU][hapmap]
rs73000182	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376741	0.82[CEU][hapmap]
rs9390074	0.83[CEU][hapmap]
rs9390075	0.83[CEU][hapmap];0.85[GIH][hapmap]
rs9390076	0.83[CEU][hapmap]
rs9399439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399440	0.89[ASN][1000 genomes]
rs9403478	0.80[CEU][hapmap]
rs9403485	0.94[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs9403486	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs9496561	0.83[CEU][hapmap]
rs9496594	0.89[EUR][1000 genomes]
rs967633	0.83[CEU][hapmap]
rs9908	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1559599	SYCE2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143642600-143675600	Weak transcription	Left Ventricle	heart
2	chr6:143643800-143661200	Weak transcription	Aorta	Aorta
3	chr6:143645000-143683200	Weak transcription	Pancreas	Pancrea
4	chr6:143646000-143664000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:143652400-143662200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:143652800-143664000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:143653000-143659000	Weak transcription	K562	blood
8	chr6:143653000-143662200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:143653000-143665600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:143653400-143663800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:143653800-143660600	Weak transcription	Fetal Stomach	stomach
12	chr6:143653800-143661000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:143653800-143663400	Weak transcription	Fetal Lung	lung
14	chr6:143654000-143672000	Weak transcription	Ovary	ovary
15	chr6:143654200-143661600	Strong transcription	Liver	Liver
16	chr6:143654400-143667800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:143654800-143663600	Weak transcription	Fetal Kidney	kidney
18	chr6:143655200-143665800	Weak transcription	Fetal Intestine Large	intestine
19	chr6:143655400-143664400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:143655400-143666000	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:143655600-143667200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:143655800-143659200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:143656200-143659200	Enhancers	HMEC	breast
24	chr6:143656200-143662600	Weak transcription	Fetal Brain Female	brain
25	chr6:143656200-143662800	Weak transcription	HepG2	liver
26	chr6:143656400-143658800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:143656800-143658600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:143656800-143659000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:143657000-143658800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:143657000-143659800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:143657200-143658400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr6:143657200-143658400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:143657200-143658600	Enhancers	HSMM	muscle
34	chr6:143657200-143658600	Enhancers	NH-A	brain
35	chr6:143657200-143658600	Enhancers	Osteobl	bone
36	chr6:143657400-143658400	Enhancers	NHDF-Ad	bronchial
37	chr6:143657400-143658400	Enhancers	NHLF	lung
38	chr6:143657400-143658600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:143657400-143658800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:143657600-143658600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr6:143657800-143658400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr6:143657800-143658400	Enhancers	HSMMtube	muscle
43	chr6:143658000-143658400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:143658000-143658800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr6:143658000-143659000	Enhancers	Placenta	Placenta
46	chr6:143658200-143658600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:143658200-143659400	Enhancers	Esophagus	oesophagus
48	chr6:143658200-143659400	Strong transcription	Fetal Intestine Small	intestine
49	chr6:143658200-143659400	Transcr. at gene 5' and 3'	NHEK	skin
50	chr6:143658200-143667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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