Variant report

Variant	rs588136
Chromosome Location	chr15:58730498-58730499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58623609..58625282-chr15:58727962..58730632,2	MCF-7	breast:
2	chr15:58729567..58734283-chr15:58741092..58746394,5	K562	blood:
3	chr15:58726654..58728474-chr15:58730449..58733344,2	MCF-7	breast:
4	chr15:58728810..58730578-chr15:58760180..58761799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1077834	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1077835	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1800588	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2070895	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs261332	0.95[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs261334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs261342	0.95[CEU][hapmap]
rs633695	0.82[CEU][hapmap]
rs8034802	0.82[CEU][hapmap]

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	esv2760372	chr15:58721447-58731153	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2761874	chr15:58724371-58730571	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv524065	chr15:58725839-58730889	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	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

Variant related diseases (count:2)

Disease	PMID	Source
Lipid traits	24023260	GWAS catalog
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs588136	RFX7	cis	parietal	SCAN
rs588136	FAM63B	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58722600-58731000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:58724600-58731000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:58724800-58731200	Weak transcription	NHDF-Ad	bronchial
4	chr15:58724800-58732600	Weak transcription	Psoas Muscle	Psoas
5	chr15:58725000-58731000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:58725000-58731000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:58725200-58732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:58725800-58731800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:58726200-58732000	Weak transcription	Fetal Intestine Small	intestine
10	chr15:58726400-58731000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:58726400-58731000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:58726400-58731000	Weak transcription	Hela-S3	cervix
13	chr15:58726400-58731200	Weak transcription	Placenta	Placenta
14	chr15:58726400-58737200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:58726600-58731000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:58726600-58731600	Weak transcription	Adipose Nuclei	Adipose
17	chr15:58726600-58732200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:58726600-58734200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:58726800-58730800	Weak transcription	Left Ventricle	heart
20	chr15:58726800-58731200	Weak transcription	HSMMtube	muscle
21	chr15:58726800-58731600	Weak transcription	Stomach Mucosa	stomach
22	chr15:58726800-58732000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:58726800-58732000	Weak transcription	HSMM	muscle
24	chr15:58727000-58731200	Weak transcription	Esophagus	oesophagus
25	chr15:58727000-58731400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:58727200-58730600	Weak transcription	Right Ventricle	heart
27	chr15:58727200-58730600	Weak transcription	Spleen	Spleen
28	chr15:58727200-58731200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:58727200-58731200	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:58727200-58731600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:58728400-58731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:58728800-58738200	Enhancers	Fetal Thymus	thymus
33	chr15:58729200-58732000	Enhancers	A549	lung
34	chr15:58729200-58733400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:58729400-58732000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:58729800-58737800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:58730000-58730600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:58730000-58732600	Weak transcription	Thymus	Thymus
39	chr15:58730000-58734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:58730000-58737800	Enhancers	HepG2	liver
41	chr15:58730200-58731000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:58730200-58731200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:58730200-58731200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:58730200-58731600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:58730200-58732200	Weak transcription	Fetal Heart	heart
46	chr15:58730200-58734400	Enhancers	Pancreas	Pancrea
47	chr15:58730400-58730800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:58730400-58731000	Weak transcription	Gastric	stomach
49	chr15:58730400-58737800	Enhancers	Right Atrium	heart
50	chr15:58730400-58738000	Enhancers	Liver	Liver

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