Variant report

Variant	rs2072532
Chromosome Location	chr2:40366301-40366302
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	chr2:40365962..40367921-chr2:40369317..40371065,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10490206	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11676744	0.92[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs11680622	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11687766	0.85[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12464756	1.00[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12466767	0.85[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12470980	0.81[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12478057	0.81[CEU][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712683	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17501526	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17559580	0.81[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17559651	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2005886	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072531	0.87[TSI][hapmap]
rs2110926	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373791	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373792	0.85[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2888657	0.89[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952354	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5542	0.89[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5551	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]
rs56090875	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62150869	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62150874	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735142	0.82[YRI][hapmap]
rs6742885	0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs929642	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv873906	chr2:40341847-40385045	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873907	chr2:40349094-40381369	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1005758	chr2:40349403-40381369	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv873908	chr2:40351453-40371095	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv873909	chr2:40358526-40371095	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072532	SOS1	cis	parietal	SCAN
rs2072532	ABCG5	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40354600-40366600	Weak transcription	Lung	lung
2	chr2:40355400-40383800	Weak transcription	Small Intestine	intestine
3	chr2:40355800-40370000	Weak transcription	Fetal Brain Male	brain
4	chr2:40356000-40367400	Weak transcription	Fetal Brain Female	brain
5	chr2:40356800-40375000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:40357600-40374000	Weak transcription	HSMMtube	muscle
7	chr2:40357800-40366600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:40358200-40392200	Weak transcription	NHLF	lung
11	chr2:40358800-40369200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:40358800-40389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:40359000-40387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:40360400-40366800	Weak transcription	Ovary	ovary
15	chr2:40361000-40375000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:40361800-40369200	Strong transcription	Dnd41	blood
17	chr2:40362400-40366400	Strong transcription	Left Ventricle	heart
18	chr2:40363800-40369200	Strong transcription	HSMM	muscle
19	chr2:40364000-40366800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr2:40364200-40367400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:40364200-40377400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:40364400-40383800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:40364600-40375000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:40364600-40387000	Weak transcription	Placenta	Placenta
25	chr2:40364800-40369200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:40364800-40380400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:40365200-40369200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:40365200-40372800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:40365400-40366600	Strong transcription	Right Ventricle	heart
31	chr2:40365400-40366800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:40365600-40366600	Strong transcription	Brain Germinal Matrix	brain
33	chr2:40365600-40366800	Strong transcription	Aorta	Aorta
34	chr2:40365600-40367000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:40365600-40367000	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:40365600-40368800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:40366000-40368400	Genic enhancers	Fetal Heart	heart
38	chr2:40366000-40368600	Strong transcription	Osteobl	bone
39	chr2:40366200-40366800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:40366200-40366800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:40366200-40367000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:40366200-40368400	Strong transcription	Fetal Stomach	stomach
43	chr2:40366200-40368800	Weak transcription	Duodenum Mucosa	Duodenum

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