Variant report

Variant	rs12650360
Chromosome Location	chr4:128544514-128544515
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	chr4:128543078..128545882-chr4:128552977..128554729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164066	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1018289	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11098931	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11098933	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11728750	0.88[ASN][1000 genomes]
rs11732886	0.92[ASN][1000 genomes]
rs12509562	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12649427	0.91[ASN][1000 genomes]
rs13151291	0.92[ASN][1000 genomes]
rs1399211	0.96[ASN][1000 genomes]
rs1459051	0.89[ASN][1000 genomes]
rs1514298	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1913464	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2048686	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2255457	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2391188	0.96[ASN][1000 genomes]
rs2391189	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34240473	0.89[ASN][1000 genomes]
rs36179490	0.91[ASN][1000 genomes]
rs4834209	0.92[ASN][1000 genomes]
rs59255549	0.91[ASN][1000 genomes]
rs62334037	0.91[ASN][1000 genomes]
rs6534631	0.95[ASN][1000 genomes]
rs6534633	0.92[ASN][1000 genomes]
rs6534634	0.92[ASN][1000 genomes]
rs6534637	0.83[ASN][1000 genomes]
rs6810904	0.92[ASN][1000 genomes]
rs6823957	0.87[ASN][1000 genomes]
rs6828511	0.91[ASN][1000 genomes]
rs6847397	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6858855	0.91[ASN][1000 genomes]
rs7686395	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs922060	0.89[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	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1800085	chr4:128502675-128557864	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128543600-128544600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
2	chr4:128543600-128545000	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr4:128543600-128545200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:128543600-128545200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr4:128543600-128545200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:128543600-128545400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:128543600-128545400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:128543600-128545600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:128543600-128545600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:128543600-128545600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:128543600-128545600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:128543600-128546000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:128543600-128546400	Active TSS	Brain Anterior Caudate	brain
14	chr4:128543800-128544600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr4:128543800-128544600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
16	chr4:128543800-128544600	Bivalent Enhancer	Liver	Liver
17	chr4:128543800-128544600	Bivalent Enhancer	Fetal Thymus	thymus
18	chr4:128543800-128544800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:128543800-128544800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:128543800-128544800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:128543800-128545000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr4:128543800-128545000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
24	chr4:128543800-128545000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:128543800-128545000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
27	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr4:128543800-128545000	Bivalent/Poised TSS	Left Ventricle	heart
31	chr4:128543800-128545000	Flanking Active TSS	Pancreas	Pancrea
32	chr4:128543800-128545000	Flanking Bivalent TSS/Enh	HepG2	liver
33	chr4:128543800-128545200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:128543800-128545200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr4:128543800-128545200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:128543800-128545200	Active TSS	Rectal Smooth Muscle	rectum
37	chr4:128543800-128545200	Active TSS	A549	lung
38	chr4:128543800-128545200	Bivalent/Poised TSS	HSMM	muscle
39	chr4:128543800-128545200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr4:128543800-128545600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr4:128543800-128545600	Active TSS	Brain Substantia Nigra	brain
42	chr4:128543800-128546600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:128543800-128547000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr4:128544000-128544600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
45	chr4:128544000-128544600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr4:128544000-128544600	Flanking Active TSS	Right Ventricle	heart
47	chr4:128544000-128544800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:128544000-128544800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr4:128544000-128544800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr4:128544000-128544800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

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