Variant report

Variant	rs627354
Chromosome Location	chr11:74028944-74028945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74020783..74024598-chr11:74028105..74031169,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246211	Chromatin interaction
ENSG00000149380	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1063807	0.91[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10793071	0.84[ASN][1000 genomes]
rs10898977	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs10898978	0.83[ASN][1000 genomes]
rs10898979	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10898982	0.88[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs12364246	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12365592	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12804647	0.80[AMR][1000 genomes]
rs1290193	0.97[AFR][1000 genomes]
rs1726744	0.89[ASW][hapmap]
rs1726746	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs1941817	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848559	0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3193507	0.91[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3867269	0.86[ASN][1000 genomes]
rs3894651	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4306310	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4641511	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474280	1.00[ASW][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs474835	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs486577	1.00[ASW][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs490539	1.00[ASW][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs500608	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs513678	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556134	0.81[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55660813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568959	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578057	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs61901471	0.81[AMR][1000 genomes]
rs634243	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs642884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106149	0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7106827	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121767	0.81[AMR][1000 genomes]
rs7130795	0.91[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs752577	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931026	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7943938	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7947390	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	esv3462630	chr11:74022904-74029002	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv555424	chr11:74025055-74028944	ZNF genes & repeats Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv555425	chr11:74025055-74034473	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv555429	chr11:74025279-74034473	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv555436	chr11:74025411-74028944	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv555442	chr11:74026090-74028944	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs627354	RP11-702H23.4	cis	Thyroid	GTEx
rs627354	HNRNPA1P40	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74023200-74036800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:74027800-74029400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr11:74028000-74031000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:74028200-74029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:74028400-74030400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:74028400-74030800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:74028400-74031000	Enhancers	Osteobl	bone
8	chr11:74028600-74030200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:74028600-74030800	Enhancers	NHDF-Ad	bronchial
10	chr11:74028600-74031000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:74028600-74031800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:74028800-74029200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:74028800-74030800	Enhancers	HSMMtube	muscle
14	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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