Variant report

Variant	rs11584499
Chromosome Location	chr1:228235809-228235810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228235239..228237153-chr1:228244250..228246467,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034792	0.92[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1048503	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10495278	1.00[ASW][hapmap]
rs10916261	0.90[EUR][1000 genomes]
rs10916262	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11577976	1.00[ASW][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap]
rs11589040	0.87[TSI][hapmap]
rs11589467	0.87[TSI][hapmap]
rs11589513	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1188975	0.86[JPT][hapmap]
rs1188977	0.86[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12033088	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048010	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13374948	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1620734	0.86[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs1745420	0.90[EUR][1000 genomes]
rs1745422	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070960	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107905	0.90[EUR][1000 genomes]
rs3738680	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738681	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768329	0.85[TSI][hapmap]
rs3795774	0.82[CHB][hapmap]
rs3820624	0.97[ASN][1000 genomes]
rs41270175	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41270177	0.96[EUR][1000 genomes]
rs4653533	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs4653897	0.96[EUR][1000 genomes]
rs57146523	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57657087	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60213528	0.85[AMR][1000 genomes]
rs61825125	0.81[EUR][1000 genomes]
rs61825130	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61825131	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825133	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825135	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61825156	0.82[ASN][1000 genomes]
rs6672422	0.87[TSI][hapmap]
rs6672559	0.87[TSI][hapmap]
rs708126	0.86[JPT][hapmap]
rs72756204	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72756209	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7539664	0.92[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs822727	0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs860301	0.80[EUR][1000 genomes]
rs882451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9287011	1.00[ASW][hapmap];0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
10	esv1814215	chr1:228231601-228259932	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	esv1844252	chr1:228231601-228259932	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
13	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
14	esv3405107	chr1:228232029-228236527	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv3356024	chr1:228233379-228235877	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11584499	LEFTY1	cis	parietal	SCAN
rs11584499	MIXL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228231400-228239600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:228234600-228238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:228235800-228236200	Enhancers	Stomach Mucosa	stomach

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