Variant report

Variant	rs5551
Chromosome Location	chr2:40339986-40339987
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	chr2:40334175..40336560-chr2:40339727..40341466,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10490206	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680622	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11687766	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12464756	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12466767	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12470980	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12478057	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712683	0.92[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13005439	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17501526	0.92[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17559580	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17559651	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2005886	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2072531	0.87[TSI][hapmap]
rs2072532	0.81[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2110926	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373791	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2373792	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888657	0.81[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4952354	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5542	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56090875	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60563966	0.94[ASN][1000 genomes]
rs62150869	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62150874	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs929642	0.96[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5551	SOS1	cis	parietal	SCAN
rs5551	ABCG5	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
2	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
3	chr2:40328000-40365600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:40329000-40341400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:40329600-40341400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:40329800-40342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:40329800-40345200	Weak transcription	Fetal Thymus	thymus
8	chr2:40331000-40340800	Weak transcription	Dnd41	blood
9	chr2:40331200-40350200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:40331200-40351200	Weak transcription	Fetal Stomach	stomach
11	chr2:40333000-40351000	Weak transcription	Aorta	Aorta
12	chr2:40333200-40342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:40333400-40340800	Weak transcription	Psoas Muscle	Psoas
14	chr2:40333400-40354400	Weak transcription	NH-A	brain
15	chr2:40333600-40340600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:40333800-40340200	Weak transcription	Osteobl	bone
17	chr2:40334600-40354800	Weak transcription	Fetal Brain Female	brain
18	chr2:40336600-40345600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:40338000-40340200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:40338200-40341400	Weak transcription	Left Ventricle	heart
21	chr2:40339000-40342600	Enhancers	NHDF-Ad	bronchial
22	chr2:40339000-40345800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:40339200-40340000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:40339200-40340200	Weak transcription	HSMM	muscle
25	chr2:40339800-40341000	Weak transcription	Fetal Heart	heart
26	chr2:40339800-40341400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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