Variant report

Variant	rs8025937
Chromosome Location	chr15:52644695-52644696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52586418..52589137-chr15:52642806..52644960,2	MCF-7	breast:
2	chr15:52642497..52646908-chr15:52859838..52862165,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12438578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441597	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900962	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12901814	0.80[ASN][1000 genomes]
rs1405183	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1405184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17707852	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs1965563	0.84[ASN][1000 genomes]
rs2290332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28533733	0.81[AMR][1000 genomes]
rs3794557	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3794564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176600	0.81[AMR][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8030535	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs871488	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs940970	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
3	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:52611800-52675800	Weak transcription	Gastric	stomach
6	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
7	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
8	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
10	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
11	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
12	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
15	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:52633600-52645400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:52635200-52648200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:52638200-52645800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr15:52640200-52646200	Strong transcription	Brain Cingulate Gyrus	brain
24	chr15:52640200-52646200	Strong transcription	Fetal Brain Female	brain
25	chr15:52640200-52646400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:52640200-52646600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:52640200-52647000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:52640200-52647600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:52640200-52655000	Weak transcription	Liver	Liver
30	chr15:52640400-52646200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52640400-52646600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52640400-52648400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr15:52640600-52646200	Strong transcription	Brain Anterior Caudate	brain
34	chr15:52640600-52646200	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:52640600-52648200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:52641200-52645800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:52641200-52646200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:52641200-52646200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:52641200-52646200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:52641200-52646200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:52641400-52644800	Strong transcription	Dnd41	blood
43	chr15:52641400-52646200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:52641400-52646200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:52641400-52646200	Strong transcription	Brain Angular Gyrus	brain
46	chr15:52641400-52646200	Strong transcription	Brain Germinal Matrix	brain
47	chr15:52641400-52646200	Strong transcription	Fetal Thymus	thymus
48	chr15:52641400-52646200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:52641400-52646200	Strong transcription	HUVEC	blood vessel
50	chr15:52641400-52646400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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