Variant report

Variant	rs3850640
Chromosome Location	chr1:172253765-172253766
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	chr1:172253395..172255527-chr1:172290385..172292894,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10489289	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489290	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489291	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489292	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10752914	0.89[EUR][1000 genomes]
rs10797881	0.89[EUR][1000 genomes]
rs10797902	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911323	0.89[EUR][1000 genomes]
rs10911326	0.89[EUR][1000 genomes]
rs10911335	0.89[EUR][1000 genomes]
rs10911336	0.89[EUR][1000 genomes]
rs10911338	0.89[EUR][1000 genomes]
rs10911349	0.89[EUR][1000 genomes]
rs10911356	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911394	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911433	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911504	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583757	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063247	0.89[EUR][1000 genomes]
rs12073843	0.89[EUR][1000 genomes]
rs12075079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12081408	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082431	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402454	1.00[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12402792	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403844	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404363	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12404490	0.94[EUR][1000 genomes]
rs12407453	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12409279	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12410143	0.89[EUR][1000 genomes]
rs12410416	1.00[CEU][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs12411264	1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs12563643	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567175	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1317394	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844126	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844128	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844133	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844134	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844255	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289635	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2422074	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2422075	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586392	0.82[CHD][hapmap]
rs2586394	0.82[CHD][hapmap]
rs2757493	0.80[CHD][hapmap]
rs2757495	0.82[JPT][hapmap]
rs3850639	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3895277	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41516352	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs4382763	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484957	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55656112	0.89[EUR][1000 genomes]
rs56682471	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60866522	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676836	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6686118	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6701414	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6701929	0.80[CHD][hapmap]
rs678962	1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72721163	0.90[EUR][1000 genomes]
rs72721182	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72721197	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72723204	0.85[EUR][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	nsv1006542	chr1:172253765-172304690	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3850640	CREG1	cis	cerebellum	SCAN
rs3850640	SELP	cis	cerebellum	SCAN
rs3850640	BRP44	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:172247800-172255800	Weak transcription	Left Ventricle	heart
3	chr1:172247800-172256000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172248200-172255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:172248200-172255400	Weak transcription	HSMM	muscle
6	chr1:172248200-172255400	Weak transcription	NHLF	lung
7	chr1:172248200-172255800	Weak transcription	Aorta	Aorta
8	chr1:172249200-172255400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:172249200-172255600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:172249400-172256000	Weak transcription	Esophagus	oesophagus
11	chr1:172249600-172255000	Weak transcription	NHDF-Ad	bronchial
12	chr1:172251800-172257000	Weak transcription	Right Ventricle	heart
13	chr1:172253000-172253800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:172253000-172253800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:172253000-172257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:172253600-172254200	Enhancers	Colon Smooth Muscle	Colon
17	chr1:172253600-172254800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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