Variant report

Variant	rs4964728
Chromosome Location	chr12:104649733-104649734
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104647499..104652832-chr12:104679215..104682822,7	K562	blood:
2	chr12:104648960..104654527-chr12:104679132..104682678,7	MCF-7	breast:
3	chr12:104648718..104651563-chr12:104680805..104682351,2	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10400561	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10735393	0.81[GIH][hapmap]
rs10745994	0.82[EUR][1000 genomes]
rs10778309	0.89[CHB][hapmap]
rs10778311	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs10778316	0.85[CHB][hapmap]
rs10778318	0.89[CHB][hapmap]
rs10778323	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs10861169	0.90[JPT][hapmap]
rs10861180	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861181	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111955	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111963	0.89[CHB][hapmap]
rs17035324	0.90[JPT][hapmap]
rs4129598	0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4246264	0.90[JPT][hapmap]
rs4388968	0.88[JPT][hapmap]
rs4406890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4545635	0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4614534	0.83[CHD][hapmap];0.87[MEX][hapmap]
rs4964260	0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4964267	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964270	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964271	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6539132	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6539138	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs7138523	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs7297560	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299866	0.88[MEX][hapmap]
rs7310505	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7342395	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs7957725	1.00[CHB][hapmap]
rs7958851	0.89[EUR][1000 genomes]
rs7960443	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975161	1.00[CEU][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4964728	C12orf48	cis	cerebellum	SCAN
rs4964728	NR1H4	cis	cerebellum	SCAN
rs4964728	CHST11	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104647400-104650000	Weak transcription	K562	blood
2	chr12:104649000-104649800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:104649200-104649800	Active TSS	Hela-S3	cervix
4	chr12:104649600-104650200	Flanking Active TSS	A549	lung

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