Variant report

Variant	rs578300
Chromosome Location	chr11:107701784-107701785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:107701670..107703248-chr11:107728191..107729812,2	MCF-7	breast:
2	chr11:107693861..107695588-chr11:107701609..107703172,2	K562	blood:
3	chr11:107693680..107695656-chr11:107699193..107701857,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110660	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10789638	0.82[ASN][1000 genomes]
rs10890769	0.81[ASN][1000 genomes]
rs10890770	0.82[ASN][1000 genomes]
rs11212405	0.81[ASN][1000 genomes]
rs11212408	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs11603925	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12221840	0.82[ASN][1000 genomes]
rs12278174	0.82[ASN][1000 genomes]
rs12418609	0.81[ASN][1000 genomes]
rs2442683	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs2510889	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3099829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3105397	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105399	0.83[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4753819	0.82[ASN][1000 genomes]
rs4753821	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4754264	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4754265	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4754267	0.80[CHB][hapmap]
rs483463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488081	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488512	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs502398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522861	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523750	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529987	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs539178	0.80[GIH][hapmap]
rs542931	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs562592	0.80[GIH][hapmap]
rs564569	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs565438	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566238	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573074	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575008	0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs579485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656220	0.80[GIH][hapmap]
rs657608	0.87[EUR][1000 genomes]
rs668785	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs7949443	0.82[ASN][1000 genomes]
rs9737154	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv427899	chr11:107471544-107805894	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1038581	chr11:107564274-107838386	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv898378	chr11:107580985-107847983	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1035229	chr11:107653731-107717190	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv1052829	chr11:107686808-107725297	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1045388	chr11:107686808-107733498	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv3417743	chr11:107699670-107725103	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107673400-107727800	Weak transcription	Primary B cells from cord blood	blood
2	chr11:107691200-107709600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:107692600-107701800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr11:107696600-107711000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:107697200-107702200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:107697200-107709800	Weak transcription	GM12878-XiMat	blood
7	chr11:107701400-107702200	Enhancers	Liver	Liver
8	chr11:107701400-107702200	Enhancers	Stomach Mucosa	stomach
9	chr11:107701400-107702200	Enhancers	A549	lung
10	chr11:107701400-107702600	Enhancers	Hela-S3	cervix
11	chr11:107701400-107703000	Enhancers	HUVEC	blood vessel
12	chr11:107701400-107703800	Enhancers	HMEC	breast
13	chr11:107701400-107704000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:107701400-107704000	Enhancers	NHEK	skin
15	chr11:107701400-107704400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:107701600-107704400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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