Variant report

Variant	rs12104503
Chromosome Location	chr2:188297133-188297134
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188276001..188278638-chr2:188296407..188297953,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10179705	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs10194145	0.82[ASN][1000 genomes]
rs10194247	0.82[ASN][1000 genomes]
rs10201618	0.80[ASN][1000 genomes]
rs10203398	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs10203781	0.82[ASN][1000 genomes]
rs10931289	0.82[ASN][1000 genomes]
rs11674362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685426	0.82[ASN][1000 genomes]
rs11691442	0.82[ASN][1000 genomes]
rs11896404	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11897572	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs11903296	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs13019491	0.82[ASN][1000 genomes]
rs13392310	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13430354	1.00[CHB][hapmap]
rs13430665	1.00[CHB][hapmap]
rs1355519	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs1355520	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1355521	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398061	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs16829016	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17367055	0.82[ASN][1000 genomes]
rs17464221	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs1912846	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912847	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912848	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1912849	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030976	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2058670	0.82[ASN][1000 genomes]
rs2349315	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2882203	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213739	0.86[GIH][hapmap]
rs3771059	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs3771061	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs3771067	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs3771073	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3771076	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771078	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs3771084	0.82[MEX][hapmap]
rs3821180	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs3821184	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4140885	1.00[CHB][hapmap]
rs6434219	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap]
rs6719550	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs67285003	0.82[ASN][1000 genomes]
rs67492154	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753700	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6759535	0.82[MEX][hapmap]
rs696092	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs698579	0.81[CHB][hapmap];0.81[MEX][hapmap]
rs698590	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs698592	1.00[CHB][hapmap]
rs72902495	0.82[ASN][1000 genomes]
rs7586970	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap]
rs7589163	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7591567	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs7598858	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap]
rs7601254	0.91[GIH][hapmap]
rs8176479	0.90[CHB][hapmap]
rs8176498	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs8176501	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs8176528	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs8176541	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap]
rs8176546	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs8176547	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8176548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8176580	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs8176583	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs8176592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap]
rs858744	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap]
rs858759	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap]
rs9288140	0.83[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv834487	chr2:188182556-188353363	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv875557	chr2:188219052-188370232	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875558	chr2:188219052-188388311	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv875559	chr2:188219052-188390112	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv584036	chr2:188256158-188369841	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875562	chr2:188258904-188370232	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv875563	chr2:188258904-188388311	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12104503	ORMDL1	cis	cerebellum	SCAN
rs12104503	CALCRL	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188269600-188309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:188269800-188308400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:188286600-188304000	Weak transcription	Psoas Muscle	Psoas
4	chr2:188295000-188298600	Weak transcription	NHLF	lung
5	chr2:188295000-188303000	Weak transcription	Brain Substantia Nigra	brain
6	chr2:188295200-188309600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:188295400-188298600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:188295400-188299000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:188295400-188299000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:188295400-188299000	Weak transcription	HSMM	muscle
11	chr2:188295400-188299000	Weak transcription	NHEK	skin
12	chr2:188295400-188299600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:188295400-188299600	Weak transcription	Osteobl	bone
14	chr2:188295400-188300800	Weak transcription	NH-A	brain
15	chr2:188295400-188301000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:188295400-188303000	Weak transcription	HSMMtube	muscle
17	chr2:188295600-188302400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:188295600-188302600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:188295800-188299400	Genic enhancers	HUVEC	blood vessel
20	chr2:188296000-188297800	Enhancers	HepG2	liver
21	chr2:188296200-188298400	Enhancers	Liver	Liver
22	chr2:188296200-188299000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:188296600-188297600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:188296600-188298400	Enhancers	Adipose Nuclei	Adipose
25	chr2:188296800-188298800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:188297000-188298800	Weak transcription	NHDF-Ad	bronchial

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