Variant report

Variant	rs12818749
Chromosome Location	chr12:31670378-31670379
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	chr12:31664969..31667862-chr12:31670364..31672875,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1038066	0.86[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1269139	0.80[EUR][1000 genomes]
rs12809140	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12812075	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12812141	0.91[CEU][hapmap]
rs12816170	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12816386	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs12819062	0.90[EUR][1000 genomes]
rs12820294	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821808	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12822601	0.93[EUR][1000 genomes]
rs12825207	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826193	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12831480	0.89[EUR][1000 genomes]
rs17497517	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497656	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497998	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126897	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34007930	0.88[EUR][1000 genomes]
rs34094545	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34184789	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34271764	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34308937	0.90[EUR][1000 genomes]
rs34450466	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34585237	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34642866	0.88[EUR][1000 genomes]
rs34667511	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34949976	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34955459	0.90[EUR][1000 genomes]
rs34986122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029695	0.92[EUR][1000 genomes]
rs35193529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35545963	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35567364	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35679974	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692484	0.92[EUR][1000 genomes]
rs3850967	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4338625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930977	1.00[MEX][hapmap]
rs4930981	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930983	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931485	0.81[EUR][1000 genomes]
rs4931498	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4931503	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931504	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931510	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55635343	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55643034	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55771933	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56183451	0.88[EUR][1000 genomes]
rs56234529	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56282720	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409505	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66479670	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66520413	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66552209	0.91[EUR][1000 genomes]
rs66597773	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66635949	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67415228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67963293	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68030436	0.86[EUR][1000 genomes]
rs71455664	0.91[EUR][1000 genomes]
rs71455667	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71455668	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71455669	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71455670	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080503	0.88[EUR][1000 genomes]
rs73084486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086471	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088505	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088597	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking 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 target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12818749	BICD1	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31658800-31671600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:31659200-31670600	Weak transcription	Fetal Intestine Small	intestine
3	chr12:31660000-31674600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:31660400-31670800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:31661800-31670800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:31662200-31671600	Weak transcription	HepG2	liver
7	chr12:31663600-31670600	Weak transcription	Left Ventricle	heart
8	chr12:31663600-31670600	Weak transcription	Psoas Muscle	Psoas
9	chr12:31663600-31670600	Weak transcription	Right Atrium	heart
10	chr12:31663600-31671200	Weak transcription	Right Ventricle	heart
11	chr12:31663600-31672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:31663800-31670400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:31663800-31670600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:31665000-31671400	Weak transcription	GM12878-XiMat	blood
15	chr12:31667200-31670600	Weak transcription	Fetal Stomach	stomach
16	chr12:31667800-31675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
18	chr12:31668600-31670400	Enhancers	Hela-S3	cervix
19	chr12:31669200-31671400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:31669800-31671800	Enhancers	Brain Germinal Matrix	brain
21	chr12:31669800-31672000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:31669800-31673600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:31669800-31677800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:31670000-31670800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:31670000-31670800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:31670000-31671200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr12:31670000-31671200	Enhancers	NHEK	skin
28	chr12:31670000-31671600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:31670000-31671600	Flanking Active TSS	A549	lung
30	chr12:31670000-31672000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:31670000-31672000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:31670000-31672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:31670000-31673200	Enhancers	NHLF	lung
34	chr12:31670000-31673400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr12:31670000-31673400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:31670000-31674800	Enhancers	HUVEC	blood vessel
37	chr12:31670000-31675400	Enhancers	Fetal Kidney	kidney
38	chr12:31670000-31675400	Enhancers	Fetal Lung	lung
39	chr12:31670000-31676400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:31670200-31670400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:31670200-31670600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:31670200-31671200	Enhancers	NH-A	brain
43	chr12:31670200-31671400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:31670200-31671400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:31670200-31671400	Enhancers	HSMMtube	muscle
46	chr12:31670200-31671800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:31670200-31672000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:31670200-31672000	Enhancers	HSMM	muscle
49	chr12:31670200-31672000	Enhancers	NHDF-Ad	bronchial
50	chr12:31670200-31672200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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