Variant report

Variant	rs28655433
Chromosome Location	chr15:78200400-78200401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs28380107	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28394183	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28401601	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28402973	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28434001	0.91[ASN][1000 genomes]
rs28598868	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28694582	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28720124	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28735336	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28743037	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179653	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038351	0.91[ASN][1000 genomes]

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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28655433	RP11-114H24.2	cis	Esophagus Muscularis	GTEx
rs28655433	RP11-114H24.2	cis	Muscle Skeletal	GTEx
rs28655433	RP11-114H24.4	cis	Thyroid	GTEx
rs28655433	RP11-114H24.2	cis	lung	GTEx
rs28655433	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs28655433	RP11-114H24.2	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78180000-78215600	Weak transcription	Right Atrium	heart
2	chr15:78188400-78200400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:78192000-78202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78197000-78201000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78197400-78200400	Weak transcription	Esophagus	oesophagus
6	chr15:78198200-78200400	Weak transcription	HSMMtube	muscle
7	chr15:78198600-78200600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:78199200-78200400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:78199400-78201600	Weak transcription	Right Ventricle	heart
10	chr15:78200000-78200400	Weak transcription	Fetal Intestine Small	intestine
11	chr15:78200200-78200400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:78200200-78200400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:78200200-78201000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:78200200-78201400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:78200200-78201600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:78200200-78203000	Enhancers	Colonic Mucosa	Colon
17	chr15:78200400-78200600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:78200400-78200600	Flanking Active TSS	Hela-S3	cervix
19	chr15:78200400-78200800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:78200400-78201200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr15:78200400-78201200	Enhancers	HSMMtube	muscle
22	chr15:78200400-78201400	Enhancers	HSMM	muscle
23	chr15:78200400-78202400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:78200400-78202800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:78200400-78202800	Enhancers	Fetal Intestine Small	intestine
26	chr15:78200400-78203200	Enhancers	Esophagus	oesophagus
27	chr15:78200400-78203200	Enhancers	Stomach Mucosa	stomach
28	chr15:78200400-78203800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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