Variant report

Variant	rs261342
Chromosome Location	chr15:58731153-58731154
allele	C/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	chr15:58729567..58734283-chr15:58741092..58746394,5	K562	blood:
3	chr15:58726654..58728474-chr15:58730449..58733344,2	MCF-7	breast:
4	chr15:58730575..58732285-chr15:58839559..58842370,2	K562	blood:
5	chr15:58709732..58712579-chr15:58730855..58732681,2	K562	blood:
6	chr15:58730817..58731598-chr22:22510997..22511880,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000233720	Chromatin interaction
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1077834	0.86[CEU][hapmap]
rs1077835	0.86[CEU][hapmap]
rs1800588	0.91[CEU][hapmap]
rs2070895	0.86[CEU][hapmap]
rs261332	0.90[CEU][hapmap]
rs261334	0.95[CEU][hapmap]
rs261341	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs588136	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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:1)

Disease	PMID	Source
Metabolite levels	23281178	GWAS catalog

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58724800-58731200	Weak transcription	NHDF-Ad	bronchial
2	chr15:58724800-58732600	Weak transcription	Psoas Muscle	Psoas
3	chr15:58725200-58732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:58725800-58731800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:58726200-58732000	Weak transcription	Fetal Intestine Small	intestine
6	chr15:58726400-58731200	Weak transcription	Placenta	Placenta
7	chr15:58726400-58737200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:58726600-58731600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:58726600-58732200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:58726600-58734200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:58726800-58731200	Weak transcription	HSMMtube	muscle
12	chr15:58726800-58731600	Weak transcription	Stomach Mucosa	stomach
13	chr15:58726800-58732000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:58726800-58732000	Weak transcription	HSMM	muscle
15	chr15:58727000-58731200	Weak transcription	Esophagus	oesophagus
16	chr15:58727000-58731400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:58727200-58731200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:58727200-58731200	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:58727200-58731600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:58728400-58731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:58728800-58738200	Enhancers	Fetal Thymus	thymus
22	chr15:58729200-58732000	Enhancers	A549	lung
23	chr15:58729200-58733400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr15:58729400-58732000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:58729800-58737800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:58730000-58732600	Weak transcription	Thymus	Thymus
27	chr15:58730000-58734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:58730000-58737800	Enhancers	HepG2	liver
29	chr15:58730200-58731200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:58730200-58731200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:58730200-58731600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:58730200-58732200	Weak transcription	Fetal Heart	heart
33	chr15:58730200-58734400	Enhancers	Pancreas	Pancrea
34	chr15:58730400-58737800	Enhancers	Right Atrium	heart
35	chr15:58730400-58738000	Enhancers	Liver	Liver
36	chr15:58730400-58746200	Weak transcription	GM12878-XiMat	blood
37	chr15:58730600-58731200	Enhancers	Spleen	Spleen
38	chr15:58730600-58732600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:58730600-58734600	Enhancers	Right Ventricle	heart
40	chr15:58730800-58735200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:58730800-58737800	Enhancers	Left Ventricle	heart
42	chr15:58731000-58731200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr15:58731000-58731200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr15:58731000-58731200	Enhancers	Gastric	stomach
45	chr15:58731000-58731400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr15:58731000-58731400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:58731000-58731400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:58731000-58731800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr15:58731000-58732000	Enhancers	Hela-S3	cervix
50	chr15:58731000-58732200	Enhancers	Fetal Muscle Trunk	muscle

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