Variant report

Variant	rs12254856
Chromosome Location	chr10:90673024-90673025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1008719	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10887867	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs10887870	0.84[EUR][1000 genomes]
rs11202890	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs11202897	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11202898	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes]
rs11202899	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11202902	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202906	0.91[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11202907	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs11591231	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11595119	0.89[CEU][hapmap]
rs11596205	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1214564	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12241401	0.98[EUR][1000 genomes]
rs12248284	0.84[CEU][hapmap]
rs12254084	0.91[CEU][hapmap]
rs12256739	0.82[TSI][hapmap]
rs12267680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1411780	1.00[CHD][hapmap]
rs1653842	1.00[CHD][hapmap]
rs17114152	0.84[CEU][hapmap]
rs17114327	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1769692	1.00[CHD][hapmap]
rs2119685	0.91[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2439707	0.91[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2481918	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs303525	1.00[CHD][hapmap]
rs303526	1.00[CHD][hapmap]
rs376036	1.00[CHD][hapmap]
rs378308	1.00[CHD][hapmap]
rs390436	1.00[CHD][hapmap]
rs407433	1.00[CHD][hapmap]
rs41284106	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41317244	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs434401	1.00[CHD][hapmap]
rs442545	1.00[CHD][hapmap]
rs4431933	0.84[CEU][hapmap]
rs451949	1.00[CHD][hapmap]
rs454439	1.00[CHD][hapmap]
rs45493098	0.98[EUR][1000 genomes]
rs56104559	0.99[EUR][1000 genomes]
rs56228317	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56268252	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57807025	0.99[EUR][1000 genomes]
rs59737591	0.99[EUR][1000 genomes]
rs66478243	0.99[EUR][1000 genomes]
rs7078383	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7085698	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7090631	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7098235	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs72809310	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809311	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809314	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809318	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809335	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809337	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809342	0.98[EUR][1000 genomes]
rs7897521	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7915393	0.91[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs988584	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12254856	MYBPC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
4	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
5	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
6	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:90655200-90701400	Weak transcription	Gastric	stomach
8	chr10:90657400-90676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr10:90657600-90675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:90657600-90677600	Weak transcription	Lung	lung
11	chr10:90657600-90686400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:90658600-90686000	Weak transcription	Brain Anterior Caudate	brain
13	chr10:90659600-90689800	Weak transcription	Esophagus	oesophagus
14	chr10:90660400-90674200	Strong transcription	Primary T cells from cord blood	blood
15	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
16	chr10:90660600-90688200	Strong transcription	Dnd41	blood
17	chr10:90661200-90676200	Strong transcription	Fetal Thymus	thymus
18	chr10:90661600-90678400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:90661600-90687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:90661600-90688800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:90661600-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:90661800-90674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:90662000-90676200	Weak transcription	NH-A	brain
24	chr10:90662000-90683000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:90662600-90687600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:90662800-90688800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr10:90663200-90674200	Strong transcription	GM12878-XiMat	blood
28	chr10:90664200-90675200	Weak transcription	Left Ventricle	heart
29	chr10:90664200-90676800	Weak transcription	NHEK	skin
30	chr10:90664200-90694600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:90664400-90673800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:90664400-90675000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr10:90664400-90679400	Weak transcription	Thymus	Thymus
34	chr10:90664400-90679600	Weak transcription	Ovary	ovary
35	chr10:90664400-90683800	Weak transcription	Colonic Mucosa	Colon
36	chr10:90664400-90685600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr10:90664400-90691200	Weak transcription	Small Intestine	intestine
38	chr10:90664400-90694800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:90664600-90685400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:90665600-90674800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr10:90666000-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:90666200-90675400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:90666800-90675200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr10:90667600-90685800	Weak transcription	Colon Smooth Muscle	Colon
45	chr10:90668200-90683200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr10:90668400-90694800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr10:90668600-90675400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:90668600-90685800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:90669000-90673600	Weak transcription	A549	lung
50	chr10:90669800-90689200	Strong transcription	Primary T cells fromperipheralblood	blood

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