Variant report

Variant	rs543399
Chromosome Location	chr15:40388067-40388068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40379880..40384314-chr15:40386410..40389357,4	K562	blood:
2	chr15:40372039..40375867-chr15:40386826..40392262,4	K562	blood:
3	chr15:40336782..40338579-chr15:40387773..40390430,2	MCF-7	breast:
4	chr15:40339113..40341248-chr15:40387682..40389325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259409	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11631335	0.89[EUR][1000 genomes]
rs12592048	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs495654	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500804	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537455	0.83[CEU][hapmap]
rs568652	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs569539	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675173	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs770470	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40374200-40388200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:40381000-40390200	Genic enhancers	Fetal Stomach	stomach
3	chr15:40381800-40390200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:40382000-40389600	Weak transcription	Aorta	Aorta
5	chr15:40383000-40388600	Enhancers	Ovary	ovary
6	chr15:40383400-40394000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40383600-40388200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:40383600-40389600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:40383600-40390400	Genic enhancers	Fetal Thymus	thymus
10	chr15:40383600-40390800	Genic enhancers	Fetal Intestine Small	intestine
11	chr15:40384000-40388800	Enhancers	Placenta	Placenta
12	chr15:40384000-40388800	Enhancers	Lung	lung
13	chr15:40384000-40389800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:40384000-40389800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:40384000-40390600	Enhancers	Primary B cells from cord blood	blood
16	chr15:40384200-40390000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:40384200-40392400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:40384400-40388400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:40384800-40388800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:40384800-40389800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:40385000-40388600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:40385000-40390600	Weak transcription	Fetal Brain Female	brain
23	chr15:40385200-40390400	Enhancers	Primary T cells from cord blood	blood
24	chr15:40385400-40389200	Weak transcription	Brain Substantia Nigra	brain
25	chr15:40385400-40390000	Weak transcription	Osteobl	bone
26	chr15:40385400-40390200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:40385600-40388600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:40385600-40389000	Weak transcription	Brain Anterior Caudate	brain
29	chr15:40385600-40389800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:40385600-40389800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:40385600-40390000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:40385600-40390200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr15:40385600-40390600	Weak transcription	Fetal Brain Male	brain
34	chr15:40385800-40388600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:40385800-40388600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:40385800-40388600	Enhancers	Fetal Heart	heart
37	chr15:40385800-40388600	Weak transcription	NH-A	brain
38	chr15:40385800-40389400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:40385800-40389600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:40385800-40390000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:40385800-40390000	Enhancers	Stomach Smooth Muscle	stomach
42	chr15:40385800-40390200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:40386000-40388400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:40386000-40388600	Weak transcription	A549	lung
45	chr15:40386000-40390000	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr15:40386000-40390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:40386000-40390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:40386200-40388400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:40386200-40388400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:40386200-40388400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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