Variant report

Variant	rs2700517
Chromosome Location	chr12:104406187-104406188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11111861	1.00[ASN][1000 genomes]
rs1125322	1.00[ASN][1000 genomes]
rs11611650	1.00[ASN][1000 genomes]
rs1165672	1.00[ASN][1000 genomes]
rs12825687	1.00[ASN][1000 genomes]
rs1385663	0.93[CEU][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs167715	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167716	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882018	1.00[ASN][1000 genomes]
rs2204802	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2243680	1.00[ASN][1000 genomes]
rs2248995	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251215	1.00[ASN][1000 genomes]
rs2252213	1.00[ASN][1000 genomes]
rs2374327	1.00[ASN][1000 genomes]
rs2439621	1.00[ASN][1000 genomes]
rs2576943	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583224	1.00[ASN][1000 genomes]
rs2583225	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs2583233	1.00[ASN][1000 genomes]
rs2583234	1.00[ASN][1000 genomes]
rs2583237	1.00[ASN][1000 genomes]
rs2583244	1.00[ASN][1000 genomes]
rs2583258	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2583274	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583278	1.00[ASN][1000 genomes]
rs2629750	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700494	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700507	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2700513	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2722177	1.00[ASN][1000 genomes]
rs2722180	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722194	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2723849	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723850	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723853	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs2723877	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs322104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322109	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35140616	1.00[ASN][1000 genomes]
rs4135039	1.00[ASN][1000 genomes]
rs4135040	1.00[ASN][1000 genomes]
rs4135047	1.00[ASN][1000 genomes]
rs4135048	1.00[ASN][1000 genomes]
rs4135050	1.00[ASN][1000 genomes]
rs4135061	1.00[ASN][1000 genomes]
rs4135062	1.00[ASN][1000 genomes]
rs4135066	1.00[ASN][1000 genomes]
rs784080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs784084	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931306	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2700517	MYBPC1	cis	parietal	SCAN
rs2700517	C12orf48	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104391200-104406200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:104391600-104406400	Weak transcription	Ovary	ovary
3	chr12:104393000-104407400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:104397200-104406200	Weak transcription	Aorta	Aorta
5	chr12:104400400-104406200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:104402200-104409600	Weak transcription	Fetal Intestine Large	intestine
7	chr12:104402600-104410200	Weak transcription	Lung	lung
8	chr12:104403000-104407400	Weak transcription	Fetal Lung	lung
9	chr12:104403000-104409000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:104404000-104410000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr12:104404200-104406400	Enhancers	NHDF-Ad	bronchial
12	chr12:104404600-104406600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:104404600-104407200	Enhancers	HSMM	muscle
14	chr12:104405000-104407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:104405200-104406600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:104405200-104409000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:104405200-104409800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:104405200-104410200	Weak transcription	NHLF	lung
19	chr12:104405400-104407800	Weak transcription	Left Ventricle	heart
20	chr12:104405600-104406200	Weak transcription	HMEC	breast
21	chr12:104405600-104406400	Weak transcription	Fetal Stomach	stomach
22	chr12:104405600-104409000	Weak transcription	Osteobl	bone
23	chr12:104405600-104414000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:104405600-104414400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:104405600-104415800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:104405800-104407200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:104405800-104407400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:104405800-104409200	Weak transcription	Hela-S3	cervix
29	chr12:104405800-104409400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:104405800-104409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:104406000-104406200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:104406000-104406400	Weak transcription	HSMMtube	muscle
33	chr12:104406000-104409000	Strong transcription	Fetal Muscle Leg	muscle

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