Variant report

Variant	rs2680340
Chromosome Location	chr15:73592793-73592794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73592525..73594597-chr15:74218850..74221269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261801	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11072407	0.82[ASN][1000 genomes]
rs11072408	0.83[ASN][1000 genomes]
rs11072411	0.90[ASN][1000 genomes]
rs11072412	0.91[ASN][1000 genomes]
rs11072415	0.83[ASN][1000 genomes]
rs12439852	0.90[ASN][1000 genomes]
rs12440576	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12442755	1.00[ASN][1000 genomes]
rs12591304	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12901272	0.80[ASN][1000 genomes]
rs1878940	0.91[ASN][1000 genomes]
rs2252725	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2292915	1.00[ASN][1000 genomes]
rs2415145	0.83[ASN][1000 genomes]
rs2415146	0.83[ASN][1000 genomes]
rs2660821	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680338	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2680341	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34456824	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35348961	0.83[ASN][1000 genomes]
rs35608416	0.82[ASN][1000 genomes]
rs35778649	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3743496	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3784795	0.89[ASN][1000 genomes]
rs3859014	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3859015	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs472681	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476846	0.83[ASN][1000 genomes]
rs4776631	0.89[ASN][1000 genomes]
rs486267	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488156	0.83[ASN][1000 genomes]
rs489531	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs491742	0.81[ASN][1000 genomes]
rs492362	0.83[ASN][1000 genomes]
rs498005	0.83[ASN][1000 genomes]
rs498868	0.82[ASN][1000 genomes]
rs519946	0.83[ASN][1000 genomes]
rs519970	0.83[ASN][1000 genomes]
rs520824	0.87[ASN][1000 genomes]
rs531019	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs549253	0.87[ASN][1000 genomes]
rs559260	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs563076	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564765	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568435	0.83[ASN][1000 genomes]
rs569532	0.82[ASN][1000 genomes]
rs570001	0.94[ASN][1000 genomes]
rs573397	0.83[ASN][1000 genomes]
rs576813	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62015498	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72741448	0.88[ASN][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	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
4	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
6	chr15:73563600-73593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
12	chr15:73574000-73596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:73576400-73594600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:73577800-73598200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:73579200-73598200	Weak transcription	Psoas Muscle	Psoas
16	chr15:73580400-73594400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:73581600-73598000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:73582000-73595200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:73582000-73598000	Weak transcription	Fetal Heart	heart
20	chr15:73582800-73596800	Strong transcription	Fetal Lung	lung
21	chr15:73583400-73597000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:73583400-73598400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:73584600-73598000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:73584800-73597000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:73585000-73599400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:73585400-73597200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:73585400-73599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:73585600-73597000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr15:73586400-73593600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:73586800-73601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:73587200-73597000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:73587200-73597000	Strong transcription	Brain Angular Gyrus	brain
33	chr15:73587400-73596600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:73587600-73597400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:73588000-73596200	Weak transcription	Primary B cells from cord blood	blood
36	chr15:73588400-73598000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:73588600-73594600	Weak transcription	HepG2	liver
38	chr15:73588600-73598200	Weak transcription	Hela-S3	cervix
39	chr15:73588600-73598600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:73588800-73597800	Weak transcription	HMEC	breast
41	chr15:73588800-73601400	Strong transcription	Fetal Intestine Large	intestine
42	chr15:73588800-73601800	Strong transcription	Fetal Intestine Small	intestine
43	chr15:73589000-73596600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:73589200-73596200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:73589200-73597200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:73589600-73593200	Weak transcription	Adipose Nuclei	Adipose
47	chr15:73590000-73597000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:73590200-73595200	Weak transcription	Fetal Brain Male	brain
49	chr15:73590400-73596600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:73590600-73596200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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