Variant report

Variant	rs12678231
Chromosome Location	chr8:64088690-64088691
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:64079501..64081804-chr8:64088536..64091643,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185728	Chromatin interaction
ENSG00000270673	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10957275	0.88[EUR][1000 genomes]
rs12056447	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12542182	0.88[EUR][1000 genomes]
rs12542741	0.87[EUR][1000 genomes]
rs12547669	0.87[EUR][1000 genomes]
rs12549833	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12550222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12550793	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12677153	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975246	0.82[EUR][1000 genomes]
rs2241753	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34803356	0.87[EUR][1000 genomes]
rs3857972	0.89[EUR][1000 genomes]
rs3929126	0.89[EUR][1000 genomes]
rs4601308	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4737633	0.81[EUR][1000 genomes]
rs4739053	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4739066	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4739068	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61223024	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6983011	0.89[EUR][1000 genomes]
rs7000495	0.89[EUR][1000 genomes]
rs7000788	0.89[EUR][1000 genomes]
rs7000927	0.89[EUR][1000 genomes]
rs7001014	0.89[EUR][1000 genomes]
rs7011111	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73254967	0.89[EUR][1000 genomes]
rs73254968	0.89[EUR][1000 genomes]
rs73684686	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73684689	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73686707	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73686709	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9643383	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9643384	0.89[EUR][1000 genomes]
rs9643556	0.89[EUR][1000 genomes]
rs9643557	0.89[EUR][1000 genomes]
rs9643558	0.89[EUR][1000 genomes]
rs9643559	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890965	chr8:64006201-64104092	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv890966	chr8:64073650-64099240	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831342	chr8:64084331-64294941	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:64082000-64092200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:64082000-64098800	Weak transcription	Esophagus	oesophagus
3	chr8:64082000-64099000	Weak transcription	Gastric	stomach
4	chr8:64082200-64088800	Weak transcription	Left Ventricle	heart
5	chr8:64082200-64092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:64082200-64098600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:64082200-64098600	Weak transcription	Lung	lung
8	chr8:64082400-64098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:64082600-64089000	Weak transcription	Fetal Stomach	stomach
10	chr8:64082600-64090200	Weak transcription	Thymus	Thymus
11	chr8:64082600-64098600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:64082600-64098600	Weak transcription	Colonic Mucosa	Colon
13	chr8:64082800-64098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr8:64083000-64098600	Weak transcription	Fetal Kidney	kidney
15	chr8:64083400-64089800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:64083400-64098600	Weak transcription	HSMMtube	muscle
17	chr8:64083400-64098800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:64083600-64092000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr8:64083600-64098600	Weak transcription	Fetal Brain Male	brain
20	chr8:64083600-64098800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr8:64083600-64098800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr8:64084000-64091000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr8:64084000-64092000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:64084000-64098800	Weak transcription	Brain Germinal Matrix	brain
25	chr8:64084200-64090400	Strong transcription	K562	blood
26	chr8:64084200-64091200	Strong transcription	Fetal Thymus	thymus
27	chr8:64084200-64091200	Strong transcription	NH-A	brain
28	chr8:64084200-64091400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr8:64084200-64091800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:64084200-64091800	Strong transcription	HSMM	muscle
31	chr8:64084200-64096200	Weak transcription	Brain Substantia Nigra	brain
32	chr8:64084200-64098600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr8:64084200-64098800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr8:64084200-64102200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:64084400-64091200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr8:64084400-64091800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr8:64084400-64091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr8:64084400-64091800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:64084400-64094200	Weak transcription	Small Intestine	intestine
40	chr8:64084400-64097200	Weak transcription	NHLF	lung
41	chr8:64084400-64098600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr8:64084400-64098600	Weak transcription	Brain Anterior Caudate	brain
43	chr8:64084400-64098600	Weak transcription	Ovary	ovary
44	chr8:64084400-64098800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr8:64084400-64099000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr8:64084600-64091000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr8:64084600-64091800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:64085000-64090000	Strong transcription	HMEC	breast
49	chr8:64085200-64088800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr8:64085200-64091800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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