Variant report

Variant	rs7550558
Chromosome Location	chr1:172248219-172248220
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172247437..172249233-chr1:172327614..172329827,2	MCF-7	breast:
2	chr1:172223524..172225386-chr1:172246377..172249330,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489289	0.81[CHD][hapmap]
rs10489290	0.81[CHD][hapmap]
rs10911387	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11808940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049422	0.93[CEU][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs12069167	0.94[ASN][1000 genomes]
rs12075079	0.81[CHD][hapmap]
rs12082431	0.80[CHD][hapmap]
rs2289635	0.81[CHD][hapmap]
rs2586389	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586401	0.94[ASN][1000 genomes]
rs2586403	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs2586404	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2586407	0.94[ASN][1000 genomes]
rs2586408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2586410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2586411	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2586412	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2586413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2757493	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs2757495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2757496	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4072117	0.81[CHD][hapmap]
rs4382763	0.80[CHD][hapmap]
rs477289	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs479336	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6678749	0.81[CHD][hapmap]
rs6701929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425545	0.80[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7550558	F5	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:172246000-172249600	Enhancers	NHDF-Ad	bronchial
3	chr1:172246200-172249200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:172246200-172249400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:172246200-172249400	Enhancers	NH-A	brain
6	chr1:172246400-172249600	Enhancers	Osteobl	bone
7	chr1:172246600-172249200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:172247000-172248400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:172247000-172249400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:172247200-172249200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:172247200-172249400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:172247200-172249400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:172247200-172249800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:172247400-172248400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:172247400-172248400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:172247400-172248800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:172247400-172249000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:172247600-172248800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:172247600-172249200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:172247600-172249400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:172247800-172255800	Weak transcription	Left Ventricle	heart
22	chr1:172247800-172256000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:172248000-172249000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:172248000-172249200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:172248000-172253600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:172248200-172248600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:172248200-172249000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:172248200-172249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:172248200-172249400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr1:172248200-172249400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:172248200-172249400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:172248200-172249800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:172248200-172252400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:172248200-172255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:172248200-172255400	Weak transcription	HSMM	muscle
36	chr1:172248200-172255400	Weak transcription	NHLF	lung
37	chr1:172248200-172255800	Weak transcription	Aorta	Aorta

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