Variant report

Variant	rs12028248
Chromosome Location	chr1:46690331-46690332
allele	C/G
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	EGR1	chr1:46690218-46690492	K562	blood:	n/a	chr1:46690356-46690369 chr1:46690359-46690368 chr1:46690355-46690370 chr1:46690358-46690368 chr1:46690356-46690369 chr1:46690357-46690368 chr1:46690356-46690369 chr1:46690356-46690370

No.	Distal block	Cell Line	Cell type
1	chr1:46597067..46599767-chr1:46689224..46690792,2	K562	blood:
2	chr1:46501151..46503873-chr1:46689820..46692443,2	MCF-7	breast:
3	chr1:46683852..46686518-chr1:46689461..46693136,3	K562	blood:
4	chr1:46688930..46690733-chr1:46697591..46699102,2	K562	blood:
5	chr1:46645973..46650649-chr1:46685566..46691437,5	MCF-7	breast:

Variant related genes	Relation type
POMGNT1	TF binding region
ENSG00000085998	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000117461	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489770	0.82[MEX][hapmap]
rs10789488	0.87[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs10890386	0.87[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890388	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs11584233	0.82[AMR][1000 genomes]
rs12044708	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12125573	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12126187	1.00[MEX][hapmap]
rs12141269	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs12141928	0.94[MEX][hapmap];0.89[TSI][hapmap]
rs12406217	0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1547180	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs2292484	0.81[CHB][hapmap]
rs2292485	0.90[CHB][hapmap]
rs2292487	0.90[CHB][hapmap]
rs4612574	0.80[AMR][1000 genomes]
rs4660918	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs4660919	0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs4660920	0.82[CEU][hapmap]
rs4660921	0.82[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs6429594	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6689182	0.83[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs6692775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696085	0.81[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]
rs7521880	0.90[CHB][hapmap]
rs7527668	0.90[CHB][hapmap]
rs7527935	0.89[CHB][hapmap]
rs7538871	0.90[CHB][hapmap]
rs7552312	0.89[CHB][hapmap]
rs953070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953823	0.90[CHB][hapmap]

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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12028248	MMACHC	cis	cerebellum	SCAN
rs12028248	NSUN4	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46673000-46712200	Weak transcription	Right Atrium	heart
2	chr1:46685000-46691400	Enhancers	Brain Hippocampus Middle	brain
3	chr1:46685400-46691600	Enhancers	Brain Substantia Nigra	brain
4	chr1:46685600-46701000	Weak transcription	Fetal Stomach	stomach
5	chr1:46686000-46694400	Weak transcription	Spleen	Spleen
6	chr1:46686800-46691800	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:46687400-46692000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:46688200-46691600	Enhancers	Brain Angular Gyrus	brain
9	chr1:46689200-46690400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:46689200-46690800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:46689400-46690400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:46689600-46690600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:46689600-46691200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:46689600-46694400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:46689600-46694400	Weak transcription	Ovary	ovary
16	chr1:46689600-46698200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:46689800-46690800	Weak transcription	Brain Anterior Caudate	brain
18	chr1:46689800-46691800	Weak transcription	Aorta	Aorta
19	chr1:46690000-46691200	Weak transcription	HepG2	liver
20	chr1:46690000-46692400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:46690000-46693000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:46690200-46690400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:46690200-46690400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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