Variant report

Variant	rs12594375
Chromosome Location	chr15:58732468-58732469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58623562..58626994-chr15:58730618..58733502,3	MCF-7	breast:
2	chr15:58731963..58734945-chr15:58743116..58746394,3	K562	blood:
3	chr15:58729567..58734283-chr15:58741092..58746394,5	K562	blood:
4	chr15:58726654..58728474-chr15:58730449..58733344,2	MCF-7	breast:
5	chr15:58709732..58712579-chr15:58730855..58732681,2	K562	blood:
6	chr15:58731261..58732919-chr15:58735065..58738026,2	K562	blood:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12438063	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs12438071	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs12439649	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17301746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs568780	0.84[JPT][hapmap]
rs6494007	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8023503	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8043310	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1043362	chr15:58726337-58756571	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv1794723	chr15:58732468-58739413	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58724800-58732600	Weak transcription	Psoas Muscle	Psoas
2	chr15:58726400-58737200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:58726600-58734200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:58728800-58738200	Enhancers	Fetal Thymus	thymus
5	chr15:58729200-58733400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:58729800-58737800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:58730000-58732600	Weak transcription	Thymus	Thymus
8	chr15:58730000-58734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:58730000-58737800	Enhancers	HepG2	liver
10	chr15:58730200-58734400	Enhancers	Pancreas	Pancrea
11	chr15:58730400-58737800	Enhancers	Right Atrium	heart
12	chr15:58730400-58738000	Enhancers	Liver	Liver
13	chr15:58730400-58746200	Weak transcription	GM12878-XiMat	blood
14	chr15:58730600-58732600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:58730600-58734600	Enhancers	Right Ventricle	heart
16	chr15:58730800-58735200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:58730800-58737800	Enhancers	Left Ventricle	heart
18	chr15:58731000-58732800	Enhancers	Duodenum Mucosa	Duodenum
19	chr15:58731000-58734400	Enhancers	Fetal Muscle Leg	muscle
20	chr15:58731000-58734400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:58731000-58735200	Enhancers	Fetal Intestine Large	intestine
22	chr15:58731000-58735600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:58731000-58735800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:58731200-58732600	Enhancers	HSMMtube	muscle
25	chr15:58731200-58733000	Weak transcription	Spleen	Spleen
26	chr15:58731200-58734600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:58731200-58734600	Enhancers	Placenta	Placenta
28	chr15:58731200-58734800	Enhancers	K562	blood
29	chr15:58731200-58735200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:58731200-58736800	Weak transcription	Gastric	stomach
31	chr15:58731200-58736800	Enhancers	NHDF-Ad	bronchial
32	chr15:58731200-58737200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:58731200-58737600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr15:58731200-58737800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:58731400-58736600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:58731400-58737000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:58731600-58734600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:58731600-58735000	Enhancers	Adipose Nuclei	Adipose
39	chr15:58731600-58735000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr15:58731600-58735800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:58731600-58737200	Enhancers	Stomach Mucosa	stomach
42	chr15:58731800-58732600	Enhancers	Brain Hippocampus Middle	brain
43	chr15:58731800-58732800	Weak transcription	Esophagus	oesophagus
44	chr15:58731800-58734200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr15:58731800-58735000	Enhancers	Small Intestine	intestine
46	chr15:58731800-58736800	Enhancers	NHLF	lung
47	chr15:58731800-58739400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:58732000-58732800	Enhancers	Ovary	ovary
49	chr15:58732000-58733200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:58732000-58733200	Enhancers	Fetal Kidney	kidney

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