Variant report

Variant	rs58251663
Chromosome Location	chr7:56111475-56111476
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	chr7:56109516..56112043-chr7:56119039..56120694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10265826	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10274148	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12154781	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12155441	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12536548	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12537948	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12668193	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12671494	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12673255	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13438048	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2014042	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242509	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28438587	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28558245	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778867	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3813505	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345511	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4424212	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4427122	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4585698	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55940597	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59723101	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947671	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6960348	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970842	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6971804	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73140779	0.97[AFR][1000 genomes]
rs73140793	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140794	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766334	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793536	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793614	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58251663	SUMF2	cis	Whole Blood	GTEx
rs58251663	SUMF2	cis	Esophagus Muscularis	GTEx
rs58251663	SUMF2	cis	lung	GTEx
rs58251663	SUMF2	cis	Artery Tibial	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56102200-56114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:56102200-56117600	Weak transcription	Gastric	stomach
3	chr7:56102200-56117600	Weak transcription	Spleen	Spleen
4	chr7:56102200-56117800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:56102200-56118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:56102400-56114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:56102400-56114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:56102400-56114200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:56102400-56114200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:56102400-56114200	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:56102400-56114200	Weak transcription	Fetal Lung	lung
12	chr7:56102400-56114200	Weak transcription	HUVEC	blood vessel
13	chr7:56102400-56114200	Weak transcription	K562	blood
14	chr7:56102400-56114200	Weak transcription	Osteobl	bone
15	chr7:56102400-56114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:56102400-56117600	Weak transcription	Brain Anterior Caudate	brain
17	chr7:56102400-56117600	Weak transcription	GM12878-XiMat	blood
18	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
19	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
20	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
24	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
25	chr7:56102400-56118000	Weak transcription	NHLF	lung
26	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:56102600-56114200	Weak transcription	HSMM	muscle
28	chr7:56102600-56114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:56102600-56114600	Weak transcription	NH-A	brain
30	chr7:56102600-56114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:56102600-56116200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:56102600-56116400	Weak transcription	HMEC	breast
33	chr7:56102600-56116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:56102600-56117000	Weak transcription	Fetal Brain Female	brain
35	chr7:56102600-56117600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:56102600-56117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:56102600-56117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:56102600-56117800	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:56102600-56118000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:56102600-56118000	Weak transcription	Right Atrium	heart
41	chr7:56102800-56118000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:56102800-56118200	Weak transcription	Primary B cells from cord blood	blood
43	chr7:56102800-56118200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:56103000-56118200	Weak transcription	Thymus	Thymus
45	chr7:56103200-56111600	Weak transcription	HepG2	liver
46	chr7:56107200-56117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:56108000-56117600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:56108000-56117600	Weak transcription	Fetal Brain Male	brain
49	chr7:56108600-56112200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:56108600-56114200	Weak transcription	A549	lung

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