Variant report

Variant	rs2971365
Chromosome Location	chr3:111051871-111051872
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	chr3:111042529..111044033-chr3:111050844..111053535,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10511294	1.00[ASN][1000 genomes]
rs11920390	0.89[ASN][1000 genomes]
rs11920391	0.89[ASN][1000 genomes]
rs12106997	1.00[ASN][1000 genomes]
rs1489030	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489031	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489032	0.97[ASN][1000 genomes]
rs1489033	0.89[ASN][1000 genomes]
rs1489034	0.89[ASN][1000 genomes]
rs1489035	0.89[ASN][1000 genomes]
rs2634552	1.00[ASN][1000 genomes]
rs2634553	1.00[ASN][1000 genomes]
rs2634554	1.00[ASN][1000 genomes]
rs2675587	1.00[ASN][1000 genomes]
rs28831219	0.86[ASN][1000 genomes]
rs28846108	0.86[ASN][1000 genomes]
rs2932047	1.00[ASN][1000 genomes]
rs2932071	1.00[ASN][1000 genomes]
rs2932074	0.96[ASN][1000 genomes]
rs2950971	0.95[ASN][1000 genomes]
rs2958079	0.97[ASN][1000 genomes]
rs2958080	1.00[ASN][1000 genomes]
rs2971363	1.00[ASN][1000 genomes]
rs2971364	1.00[ASN][1000 genomes]
rs2971366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145124	1.00[ASN][1000 genomes]
rs6808323	0.86[ASN][1000 genomes]
rs7620684	0.86[ASN][1000 genomes]
rs7621095	0.86[ASN][1000 genomes]
rs7624812	0.89[ASN][1000 genomes]
rs7636637	0.89[ASN][1000 genomes]
rs9837511	0.83[ASN][1000 genomes]
rs9854335	0.89[ASN][1000 genomes]
rs9868323	0.89[ASN][1000 genomes]
rs9878888	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv963486	chr3:111047149-111055574	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2971365	SYCE1	trans	cerebellum	SCAN
rs2971365	PHLDB2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111043800-111052200	Weak transcription	HMEC	breast
2	chr3:111045800-111054400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:111050800-111052800	Enhancers	Dnd41	blood
4	chr3:111051200-111052800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:111051400-111052000	Enhancers	Fetal Thymus	thymus
6	chr3:111051400-111052200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:111051400-111053200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:111051400-111053200	Enhancers	HSMMtube	muscle
9	chr3:111051600-111052000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111051600-111052000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:111051600-111052000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:111051600-111052000	Enhancers	Fetal Muscle Leg	muscle
13	chr3:111051600-111053200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:111051600-111053200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:111051600-111053200	Enhancers	HSMM	muscle
16	chr3:111051800-111052000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:111051800-111052000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:111051800-111052000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:111051800-111052000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:111051800-111052000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:111051800-111052000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:111051800-111053200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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