Variant report

Variant	rs12466767
Chromosome Location	chr2:40349757-40349758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10490206	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676744	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680622	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11687766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12464756	0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12470980	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478057	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712683	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13005439	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17501526	0.85[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17559580	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17559651	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2005886	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2072531	0.91[TSI][hapmap]
rs2072532	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]
rs2110926	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373791	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2888657	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952354	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5542	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5551	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]
rs56090875	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60563966	0.91[ASN][1000 genomes]
rs62150869	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62150874	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742885	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs929642	0.89[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	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
10	nsv873905	chr2:40341847-40364895	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12466767	ABCG5	cis	parietal	SCAN
rs12466767	SOS1	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr2:40331200-40350200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:40331200-40351200	Weak transcription	Fetal Stomach	stomach
6	chr2:40333000-40351000	Weak transcription	Aorta	Aorta
7	chr2:40333400-40354400	Weak transcription	NH-A	brain
8	chr2:40334600-40354800	Weak transcription	Fetal Brain Female	brain
9	chr2:40340600-40351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:40340800-40350000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:40341600-40350200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:40341600-40357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:40341800-40350800	Weak transcription	Right Atrium	heart
14	chr2:40342400-40349800	Weak transcription	Osteobl	bone
15	chr2:40342800-40357600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:40343000-40350200	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:40343000-40351000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:40343000-40354800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:40343400-40350600	Weak transcription	Dnd41	blood
20	chr2:40345000-40350400	Weak transcription	HSMM	muscle
21	chr2:40345200-40350200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:40345600-40349800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:40346400-40350000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:40347000-40355800	Enhancers	Fetal Thymus	thymus
25	chr2:40347600-40350400	Weak transcription	HSMMtube	muscle
26	chr2:40347600-40354000	Weak transcription	Left Ventricle	heart
27	chr2:40349200-40350000	Enhancers	Thymus	Thymus
28	chr2:40349600-40350400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:40349600-40351600	Enhancers	Stomach Mucosa	stomach
30	chr2:40349600-40352600	Genic enhancers	Fetal Heart	heart

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