Variant report

Variant	rs55660813
Chromosome Location	chr11:74031688-74031689
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73994107..73996147-chr11:74030507..74033289,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1063807	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10793071	0.84[ASN][1000 genomes]
rs10898977	0.94[ASN][1000 genomes]
rs10898978	0.83[ASN][1000 genomes]
rs10898979	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10898982	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]
rs1941817	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848559	0.87[AFR][1000 genomes]
rs3193507	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	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474280	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs486577	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs490539	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs513678	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556134	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs568959	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578057	0.80[EUR][1000 genomes]
rs61901471	0.81[AMR][1000 genomes]
rs627354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.81[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]
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:7 , 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	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55660813	HNRNPA1P40	cis	Thyroid	GTEx
rs55660813	RP11-702H23.4	cis	Thyroid	GTEx

Chromatin state (count:36 , 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	chr11:74028600-74031800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:74029000-74034400	Enhancers	HUVEC	blood vessel
5	chr11:74029200-74032000	Enhancers	NHEK	skin
6	chr11:74029400-74031800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:74029400-74031800	Enhancers	HMEC	breast
8	chr11:74029400-74032800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:74029600-74032000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:74029800-74032000	Weak transcription	Psoas Muscle	Psoas
11	chr11:74029800-74032600	Weak transcription	Left Ventricle	heart
12	chr11:74029800-74032600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:74029800-74032800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:74029800-74033000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:74030200-74034400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr11:74030200-74035400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:74030400-74032800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:74030400-74032800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:74030600-74032200	Weak transcription	A549	lung
20	chr11:74030600-74033200	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:74030800-74032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:74030800-74032600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:74030800-74032800	Weak transcription	HSMMtube	muscle
24	chr11:74030800-74032800	Weak transcription	NH-A	brain
25	chr11:74030800-74036600	Weak transcription	HSMM	muscle
26	chr11:74030800-74037200	Weak transcription	Aorta	Aorta
27	chr11:74031200-74033800	Weak transcription	Lung	lung
28	chr11:74031200-74036200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:74031400-74032000	Enhancers	Hela-S3	cervix
31	chr11:74031400-74032200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:74031400-74034400	Enhancers	Osteobl	bone
33	chr11:74031400-74034600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:74031600-74031800	Enhancers	NHLF	lung
35	chr11:74031600-74033000	Enhancers	NHDF-Ad	bronchial
36	chr11:74031600-74034600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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