Variant report

Variant	rs7539664
Chromosome Location	chr1:228227477-228227478
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228226578..228229200-chr1:228230155..228231993,2	MCF-7	breast:
2	chr1:228225342..228227954-chr1:228229065..228231428,3	MCF-7	breast:
3	chr1:228226049..228228147-chr1:228233323..228235201,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1034792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1048503	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10916261	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916262	0.92[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11579417	0.83[CEU][hapmap]
rs11584499	0.92[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11589040	0.87[TSI][hapmap]
rs11589467	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs11589513	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1188975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1188977	0.83[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs12033088	0.89[EUR][1000 genomes]
rs12048010	0.87[EUR][1000 genomes]
rs13374948	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1342351	0.84[EUR][1000 genomes]
rs1620734	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1745420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1745422	0.89[EUR][1000 genomes]
rs2107905	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738680	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs3738681	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs3768329	0.85[TSI][hapmap]
rs41270175	0.89[EUR][1000 genomes]
rs41270177	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4363416	0.83[EUR][1000 genomes]
rs4653533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4653894	0.83[CEU][hapmap]
rs4653897	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653906	0.92[CHB][hapmap]
rs57146523	0.87[EUR][1000 genomes]
rs57556486	0.84[EUR][1000 genomes]
rs57657087	0.87[EUR][1000 genomes]
rs60213528	0.83[EUR][1000 genomes]
rs61825125	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61825130	0.87[EUR][1000 genomes]
rs61825131	0.89[EUR][1000 genomes]
rs61825133	0.83[EUR][1000 genomes]
rs6665129	0.83[CEU][hapmap]
rs6668719	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap]
rs6672422	0.83[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6672559	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs6672601	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs708126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs72756204	0.87[EUR][1000 genomes]
rs72756209	0.83[EUR][1000 genomes]
rs73110722	0.84[EUR][1000 genomes]
rs7530812	0.81[EUR][1000 genomes]
rs7537552	0.92[CHB][hapmap];0.83[LWK][hapmap]
rs822727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs860301	0.82[ASN][1000 genomes]
rs882451	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7539664	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228225800-228227800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:228225800-228231400	Weak transcription	Right Atrium	heart
3	chr1:228226200-228227600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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