Variant report

Variant	rs12593566
Chromosome Location	chr15:75310075-75310076
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75307941..75311039-chr15:75492807..75495397,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12050820	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12900654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909515	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12912959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917120	0.83[YRI][hapmap]
rs13056	0.82[YRI][hapmap]
rs1561894	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs17422130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1867151	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2083730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2120019	0.83[YRI][hapmap]
rs2304899	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs3812944	0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4627301	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4886651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4886652	0.84[AFR][1000 genomes]
rs59152319	0.96[ASN][1000 genomes]
rs59307715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495141	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6495143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7163636	0.89[YRI][hapmap]
rs7172565	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs8028632	0.83[YRI][hapmap]
rs8030089	0.81[YRI][hapmap]
rs8039755	0.90[YRI][hapmap]

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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
3	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
4	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
6	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
8	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
9	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
10	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
15	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
18	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:75304800-75310200	Strong transcription	Brain Angular Gyrus	brain
20	chr15:75304800-75312600	Strong transcription	Brain Anterior Caudate	brain
21	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
23	chr15:75305600-75310800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:75305600-75311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:75306000-75312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
27	chr15:75307600-75310800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:75307800-75315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:75308200-75310400	Strong transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:75308200-75315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:75308400-75310200	Strong transcription	HepG2	liver
32	chr15:75308600-75310200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:75308600-75311200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr15:75308600-75313800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:75308800-75310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:75308800-75312800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr15:75309000-75312600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:75309000-75315800	Weak transcription	Placenta	Placenta
39	chr15:75309200-75310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:75309200-75310800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:75309200-75311400	Strong transcription	Fetal Intestine Large	intestine
42	chr15:75309200-75311600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:75309400-75311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:75309400-75311400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:75309400-75312600	Strong transcription	Gastric	stomach
46	chr15:75309400-75315600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:75309600-75311000	Strong transcription	Pancreas	Pancrea
48	chr15:75309600-75311200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:75309800-75310800	Genic enhancers	Brain Germinal Matrix	brain
50	chr15:75309800-75313600	Strong transcription	Brain Hippocampus Middle	brain

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