Variant report

Variant	rs4546474
Chromosome Location	chr6:27224633-27224634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27223122..27224821-chr6:27228134..27229686,2	MCF-7	breast:
2	chr6:27217286..27218875-chr6:27223685..27226210,2	MCF-7	breast:
3	chr6:27224017..27225773-chr6:27244646..27246802,2	MCF-7	breast:
4	chr6:27222641..27225351-chr6:27234426..27236838,2	MCF-7	breast:
5	chr6:27223361..27225810-chr6:27777167..27778731,2	K562	blood:
6	chr6:27223940..27226636-chr6:27509869..27512543,2	K562	blood:

Variant related genes	Relation type
ENSG00000270935	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000112812	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10946904	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1156086	0.85[ASN][1000 genomes]
rs2142686	0.81[ASN][1000 genomes]
rs2295603	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594674	0.87[ASN][1000 genomes]
rs2893911	0.81[CEU][hapmap]
rs3800309	0.87[ASN][1000 genomes]
rs3800314	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800319	0.81[CEU][hapmap]
rs4236043	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4559087	0.85[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs4713074	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs5030956	0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6902268	0.85[ASN][1000 genomes]
rs6916555	0.85[ASN][1000 genomes]
rs6917311	0.87[ASN][1000 genomes]
rs6940384	0.87[ASN][1000 genomes]
rs7746841	0.80[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap]
rs9366689	0.81[CEU][hapmap]
rs9368501	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap]
rs9379968	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9468009	0.83[ASN][1000 genomes]
rs9468010	0.84[ASN][1000 genomes]
rs9468013	0.85[ASN][1000 genomes]
rs9468015	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs996247	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4546474	ZNF204P	cis	cerebellum	SCAN
rs4546474	HIST1H2BM	cis	cerebellum	SCAN
rs4546474	BTN3A2	cis	lymphoblastoid	seeQTL
rs4546474	BTN3A3	cis	cerebellum	SCAN
rs4546474	ZKSCAN3	cis	parietal	SCAN
rs4546474	ZNF323	cis	parietal	SCAN
rs4546474	HMGN4	cis	lymphoblastoid	seeQTL
rs4546474	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27220000-27225000	Weak transcription	Esophagus	oesophagus
2	chr6:27220000-27226000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:27220000-27228000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27220000-27228000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27220200-27226800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:27220200-27227800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:27220200-27228000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27220200-27228200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:27220400-27228000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:27220400-27228200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:27220600-27231600	Weak transcription	K562	blood
12	chr6:27221000-27228800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:27222400-27226000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:27223200-27226000	Weak transcription	Pancreas	Pancrea

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