Variant report

Variant	rs12915400
Chromosome Location	chr15:78201779-78201780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12901728	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12902025	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902026	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902074	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902113	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902229	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902944	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907152	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908180	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908306	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908320	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12909639	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910067	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910712	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911037	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911476	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914617	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916026	0.81[ASN][1000 genomes]
rs12916202	0.80[AFR][1000 genomes]
rs12916217	0.81[AMR][1000 genomes]
rs28479215	0.83[ASN][1000 genomes]
rs28699675	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28735336	0.82[AFR][1000 genomes]
rs3902971	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077696	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4301995	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4325521	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4325522	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4402533	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71398986	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7403058	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032772	0.88[EUR][1000 genomes];0.86[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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv833062	chr15:78035206-78220358	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904427	chr15:78129964-78251431	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv976954	chr15:78153346-78255825	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1046383	chr15:78153850-78229596	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv904428	chr15:78156238-78230906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv904429	chr15:78160362-78251431	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1827357	chr15:78200594-78206047	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1823600	chr15:78200594-78219757	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12915400	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs12915400	RP11-114H24.2	cis	Artery Aorta	GTEx
rs12915400	RP11-114H24.2	cis	Artery Tibial	GTEx
rs12915400	RP11-114H24.2	cis	Esophagus Muscularis	GTEx
rs12915400	RP11-114H24.2	cis	Thyroid	GTEx
rs12915400	RP11-114H24.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78180000-78215600	Weak transcription	Right Atrium	heart
2	chr15:78192000-78202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:78200200-78203000	Enhancers	Colonic Mucosa	Colon
4	chr15:78200400-78202400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:78200400-78202800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:78200400-78202800	Enhancers	Fetal Intestine Small	intestine
7	chr15:78200400-78203200	Enhancers	Esophagus	oesophagus
8	chr15:78200400-78203200	Enhancers	Stomach Mucosa	stomach
9	chr15:78200400-78203800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:78200600-78201800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:78200600-78202000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:78200600-78202800	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:78200800-78201800	Bivalent Enhancer	Placenta	Placenta
14	chr15:78200800-78202800	Enhancers	Fetal Intestine Large	intestine
15	chr15:78200800-78202800	Enhancers	A549	lung
16	chr15:78201000-78202800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:78201000-78202800	Weak transcription	Fetal Thymus	thymus
18	chr15:78201200-78202600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:78201200-78202600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:78201200-78202800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:78201200-78202800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:78201200-78202800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:78201200-78202800	Weak transcription	NH-A	brain
24	chr15:78201400-78202400	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:78201400-78202400	Enhancers	Hela-S3	cervix
26	chr15:78201400-78202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:78201400-78202600	Weak transcription	HepG2	liver
28	chr15:78201400-78202800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:78201400-78202800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:78201400-78202800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:78201400-78202800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:78201400-78202800	Weak transcription	HSMM	muscle
33	chr15:78201600-78201800	Enhancers	Right Ventricle	heart
34	chr15:78201600-78202200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:78201600-78202200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:78201600-78202800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:78201600-78202800	Enhancers	Duodenum Mucosa	Duodenum

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