Variant report

Variant	rs12229524
Chromosome Location	chr12:49585353-49585354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:49579315-49585380	H1-neurons	neurons:	n/a	chr12:49581154-49581167 chr12:49581154-49581167 chr12:49581714-49581734 chr12:49582472-49582485 chr12:49581151-49581171 chr12:49580352-49580362 chr12:49581151-49581171 chr12:49580345-49580358

No.	Distal block	Cell Line	Cell type
1	chr12:49503855..49506778-chr12:49583958..49586490,2	K562	blood:
2	chr12:49583300..49585414-chr12:49665857..49667533,2	K562	blood:
3	chr12:49522685..49527255-chr12:49580115..49585539,18	MCF-7	breast:
4	chr12:49584778..49586997-chr12:49594465..49596550,2	K562	blood:

Variant related genes	Relation type
TUBA1A	TF binding region
ENSG00000258017	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1039225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056875	0.82[EUR][1000 genomes]
rs1057548	0.81[EUR][1000 genomes]
rs10747561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs10747562	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10747563	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs10783306	0.80[EUR][1000 genomes]
rs10783307	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783308	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875922	0.87[EUR][1000 genomes]
rs10875924	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875925	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875927	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875928	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875929	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875930	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875931	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875934	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs11168857	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs11168862	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11168867	0.80[EUR][1000 genomes]
rs11168874	0.90[EUR][1000 genomes]
rs11168882	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168883	0.85[EUR][1000 genomes]
rs11168884	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168885	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168888	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168890	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168893	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs11168894	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168895	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168901	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168902	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168903	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168904	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168909	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168912	0.80[EUR][1000 genomes]
rs11837207	0.81[EUR][1000 genomes]
rs12227296	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12227610	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12227770	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229529	0.88[EUR][1000 genomes]
rs12306494	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12318740	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579015	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1476137	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1476138	0.83[EUR][1000 genomes]
rs1874908	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991427	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991428	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2016107	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2047101	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2114845	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2114846	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162643	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2162644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241727	0.86[EUR][1000 genomes]
rs2279596	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs2334930	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2334931	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2878287	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35884657	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741621	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs57853986	0.82[EUR][1000 genomes]
rs58336603	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58711211	0.85[EUR][1000 genomes]
rs6580701	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580703	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs697624	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7137978	0.84[EUR][1000 genomes]
rs7306084	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs73110168	0.88[EUR][1000 genomes]
rs7311346	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs731350	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7953169	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954521	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954530	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958241	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs7958572	0.88[CEU][hapmap]
rs7959497	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap]
rs7969963	0.85[EUR][1000 genomes]
rs7969967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7976890	0.81[EUR][1000 genomes]
rs7978448	0.96[CEU][hapmap]
rs9325145	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs9739878	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788139	0.84[EUR][1000 genomes]
rs9788140	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12229524	METTL7A	cis	parietal	SCAN
rs12229524	RHEBL1	cis	parietal	SCAN
rs12229524	OR10AD1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49583000-49592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:49583200-49595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:49583400-49591400	Weak transcription	K562	blood
4	chr12:49583400-49595800	Weak transcription	Ovary	ovary
5	chr12:49583600-49588800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:49583600-49592200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:49583600-49592400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:49583600-49592400	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:49583600-49594600	Weak transcription	Fetal Kidney	kidney
10	chr12:49583600-49595800	Weak transcription	Aorta	Aorta
11	chr12:49583600-49595800	Weak transcription	Fetal Thymus	thymus
12	chr12:49583800-49589200	Weak transcription	Adipose Nuclei	Adipose
13	chr12:49583800-49592400	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:49583800-49592400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:49584000-49589400	Weak transcription	Primary B cells from cord blood	blood
16	chr12:49584000-49592200	Weak transcription	NHLF	lung
17	chr12:49584200-49588800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:49584200-49588800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:49584200-49589000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:49584200-49589600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49584200-49591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:49584200-49591200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:49584200-49591200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:49584200-49594200	Weak transcription	A549	lung
25	chr12:49584400-49585600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:49584400-49585600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:49584400-49591200	Weak transcription	Brain Angular Gyrus	brain
28	chr12:49584400-49591200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:49584400-49592000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:49584400-49592400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:49584600-49589000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:49584600-49591400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:49584600-49592400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:49584600-49592400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:49584800-49585600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:49585000-49591000	Weak transcription	Brain Germinal Matrix	brain
37	chr12:49585200-49585400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:49585200-49589400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:49585200-49591000	Weak transcription	Fetal Brain Female	brain
40	chr12:49585200-49592200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:49585200-49592200	Weak transcription	Fetal Brain Male	brain

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