Variant report

Variant	rs2002651
Chromosome Location	chr7:56109770-56109771
allele	C/G
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
ENSG00000146733	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10081373	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10258800	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11238389	0.82[ASN][1000 genomes]
rs11238394	0.84[AMR][1000 genomes]
rs11771788	0.89[ASN][1000 genomes]
rs11773374	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11773453	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12537943	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12669623	0.94[ASN][1000 genomes]
rs13234899	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13240915	0.86[ASN][1000 genomes]
rs13241866	0.86[ASN][1000 genomes]
rs13242830	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13244654	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894832	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2016482	0.80[AMR][1000 genomes]
rs2016724	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230197	0.93[ASN][1000 genomes]
rs2242508	0.95[ASN][1000 genomes]
rs2331180	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2538047	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2908543	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908544	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908545	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2908550	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3735665	0.93[ASN][1000 genomes]
rs4049337	0.85[ASN][1000 genomes]
rs4275190	0.94[ASN][1000 genomes]
rs4947536	0.80[AMR][1000 genomes]
rs4948102	0.86[ASN][1000 genomes]
rs4948104	0.94[ASN][1000 genomes]
rs4948106	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62457261	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6593297	0.82[ASN][1000 genomes]
rs6945795	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6954546	0.89[ASN][1000 genomes]
rs6955423	0.86[ASN][1000 genomes]
rs6958480	0.96[ASN][1000 genomes]
rs6966609	0.89[ASN][1000 genomes]
rs766333	0.95[ASN][1000 genomes]
rs7776550	0.84[ASN][1000 genomes]
rs7782243	0.80[AMR][1000 genomes]
rs7783339	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7799471	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7801467	0.89[ASN][1000 genomes]
rs7811270	0.94[ASN][1000 genomes]
rs7811755	0.86[ASN][1000 genomes]
rs816408	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816409	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816411	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs933466	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9767946	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:93 , 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	chr7:56102400-56110000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:56102400-56110000	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:56102400-56110000	Weak transcription	NHEK	skin
9	chr7:56102400-56110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:56102400-56114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:56102400-56114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:56102400-56114200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:56102400-56114200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:56102400-56114200	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:56102400-56114200	Weak transcription	Fetal Lung	lung
16	chr7:56102400-56114200	Weak transcription	HUVEC	blood vessel
17	chr7:56102400-56114200	Weak transcription	K562	blood
18	chr7:56102400-56114200	Weak transcription	Osteobl	bone
19	chr7:56102400-56114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:56102400-56117600	Weak transcription	Brain Anterior Caudate	brain
21	chr7:56102400-56117600	Weak transcription	GM12878-XiMat	blood
22	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
23	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
24	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
28	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
29	chr7:56102400-56118000	Weak transcription	NHLF	lung
30	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:56102600-56110000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:56102600-56110000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:56102600-56110000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:56102600-56110000	Weak transcription	Primary T cells from cord blood	blood
35	chr7:56102600-56110000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:56102600-56110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:56102600-56110000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:56102600-56110000	Weak transcription	Liver	Liver
39	chr7:56102600-56110000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:56102600-56114200	Weak transcription	HSMM	muscle
41	chr7:56102600-56114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:56102600-56114600	Weak transcription	NH-A	brain
43	chr7:56102600-56114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:56102600-56116200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:56102600-56116400	Weak transcription	HMEC	breast
46	chr7:56102600-56116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:56102600-56117000	Weak transcription	Fetal Brain Female	brain
48	chr7:56102600-56117600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:56102600-56117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:56102600-56117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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