Variant report

Variant	rs2780864
Chromosome Location	chr1:56903370-56903371
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56898942..56900515-chr1:56902397..56903937,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11206807	0.95[EUR][1000 genomes]
rs11206808	0.95[EUR][1000 genomes]
rs12063481	1.00[JPT][hapmap]
rs12075340	1.00[JPT][hapmap]
rs12563470	1.00[JPT][hapmap]
rs2780865	0.93[EUR][1000 genomes]
rs72662266	0.93[EUR][1000 genomes]
rs72662267	0.95[EUR][1000 genomes]
rs914836	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs914837	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56891200-56903400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:56896600-56904200	Enhancers	Brain Angular Gyrus	brain
3	chr1:56897200-56906000	Enhancers	Brain Anterior Caudate	brain
4	chr1:56897200-56906000	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:56897200-56906000	Enhancers	Brain Substantia Nigra	brain
6	chr1:56897600-56904200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:56898000-56904000	Enhancers	Fetal Intestine Large	intestine
8	chr1:56898000-56904000	Enhancers	Fetal Intestine Small	intestine
9	chr1:56898000-56906400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:56898200-56904800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:56898600-56904000	Weak transcription	Psoas Muscle	Psoas
12	chr1:56899000-56903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:56899000-56905000	Weak transcription	Adipose Nuclei	Adipose
14	chr1:56899000-56906000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:56899400-56903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:56899400-56904000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:56899400-56904800	Weak transcription	Liver	Liver
18	chr1:56899600-56903600	Enhancers	Placenta	Placenta
19	chr1:56900200-56903400	Enhancers	Fetal Stomach	stomach
20	chr1:56900200-56903800	Weak transcription	HUVEC	blood vessel
21	chr1:56900200-56905600	Enhancers	Left Ventricle	heart
22	chr1:56900400-56904200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:56900400-56904200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:56900400-56906000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:56900400-56906400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:56900600-56904000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:56900600-56904200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:56900600-56905000	Weak transcription	Gastric	stomach
29	chr1:56900600-56912000	Weak transcription	Esophagus	oesophagus
30	chr1:56901000-56903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:56901000-56904200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:56901200-56904200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:56901800-56903800	Weak transcription	Stomach Mucosa	stomach
34	chr1:56901800-56905400	Weak transcription	Fetal Thymus	thymus
35	chr1:56901800-56906000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:56902000-56905200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:56902000-56905600	Weak transcription	Primary B cells from cord blood	blood
38	chr1:56902000-56912200	Weak transcription	Lung	lung
39	chr1:56902200-56903600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr1:56902200-56904000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:56902200-56904200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:56902200-56905400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:56902200-56911800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:56902400-56904400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:56902400-56906200	Enhancers	Brain Hippocampus Middle	brain
46	chr1:56902400-56907200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:56902600-56903400	Enhancers	Fetal Kidney	kidney
48	chr1:56902800-56903400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:56903000-56903400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:56903000-56903400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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