Variant report

Variant	rs28722697
Chromosome Location	chr15:78237071-78237072
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr15:78236641-78237276	GM12878	blood:	n/a	n/a
2	MAX	chr15:78236820-78237087	K562	blood:	n/a	chr15:78236998-78237008
3	POLR2A	chr15:78236781-78237152	SK-N-SH	brain:	n/a	n/a
4	PAX5	chr15:78236633-78237289	GM12878	blood:	n/a	n/a
5	FOSL2	chr15:78236717-78237190	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:78236738-78237195	GM12892	blood:	n/a	n/a
7	ZNF263	chr15:78236779-78237148	HEK293-T-REx	kidney:	n/a	n/a
8	POLR2A	chr15:78236761-78237181	PBDE	blood:	n/a	n/a
9	SP1	chr15:78236861-78237145	GM12878	blood:	n/a	chr15:78236998-78237007 chr15:78236997-78237009 chr15:78236997-78237009 chr15:78236998-78237008 chr15:78236994-78237008 chr15:78236999-78237008
10	JUND	chr15:78236712-78237139	K562	blood:	n/a	n/a
11	E2F6	chr15:78236693-78237156	K562	blood:	n/a	chr15:78237002-78237012
12	POLR2A	chr15:78236726-78237236	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr15:78236745-78237281	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:78236738-78237152	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:78236689-78237141	GM12878	blood:	n/a	n/a
16	TCF12	chr15:78236773-78237193	GM12878	blood:	n/a	n/a
17	HDAC2	chr15:78236654-78237080	HepG2	liver:	n/a	n/a
18	ELF1	chr15:78236798-78237117	MCF-7	breast:	n/a	n/a
19	REST	chr15:78236772-78237101	HepG2	liver:	n/a	chr15:78237022-78237032 chr15:78237076-78237089
20	BCL11A	chr15:78236927-78237145	GM12878	blood:	n/a	n/a
21	TAF1	chr15:78236679-78237156	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:78236711-78237260	GM12891	blood:	n/a	n/a
23	MAZ	chr15:78236645-78237172	K562	blood:	n/a	chr15:78236998-78237008 chr15:78236656-78236666
24	TAF1	chr15:78236842-78237174	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr15:78236730-78237175	GM19099	blood:	n/a	n/a
26	POLR2A	chr15:78236568-78237133	HepG2	liver:	n/a	n/a
27	JUND	chr15:78236801-78237085	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:78236717-78237242	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr15:78236635-78237322	PANC-1	pancreas:	n/a	n/a
30	FOXA1	chr15:78236615-78237108	HepG2	liver:	n/a	n/a
31	POLR2A	chr15:78236826-78237225	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr15:78236714-78237256	U87	brain:	n/a	n/a
33	USF1	chr15:78236745-78237155	GM12878	blood:	n/a	chr15:78236967-78236978
34	PAX5	chr15:78236855-78237096	GM12878	blood:	n/a	n/a
35	RXRA	chr15:78236646-78237206	HepG2	liver:	n/a	n/a
36	ZNF384	chr15:78236970-78237077	GM12878	blood:	n/a	n/a
37	TAF1	chr15:78236956-78237169	GM12892	blood:	n/a	n/a
38	GABPA	chr15:78236807-78237134	K562	blood:	n/a	n/a
39	CHD2	chr15:78236724-78237087	K562	blood:	n/a	n/a
40	BHLHE40	chr15:78236789-78237097	K562	blood:	n/a	n/a
41	MYBL2	chr15:78236625-78237197	HepG2	liver:	n/a	n/a
42	TCF12	chr15:78236716-78237156	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:78236770-78237171	ProgFib	skin:	n/a	n/a
44	POLR2A	chr15:78236729-78237091	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr15:78236755-78237262	GM12878	blood:	n/a	n/a
46	TAF1	chr15:78236770-78237161	GM12878	blood:	n/a	n/a
47	RXRA	chr15:78236801-78237149	GM12878	blood:	n/a	n/a
48	HCFC1	chr15:78236881-78237266	Hela-S3	cervix:	n/a	n/a
49	ZNF384	chr15:78236972-78237119	K562	blood:	n/a	n/a
50	NFIC	chr15:78236740-78237072	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78232364..78235120-chr15:78235300..78238762,3	K562	blood:
2	chr15:78236783..78237478-chrX:151999319..151999901,2	NB4	blood:

Variant related genes	Relation type
ENSG00000214646	TF binding region
ENSG00000147383	Chromatin interaction
ENSG00000214646	Chromatin interaction
ENSG00000147400	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11854044	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60257193	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72732513	0.87[AMR][1000 genomes]
rs72732516	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28722697	RP11-114H24.2	cis	Artery Tibial	GTEx
rs28722697	RP11-114H24.2	cis	Stomach	GTEx
rs28722697	RP11-114H24.2	cis	Muscle Skeletal	GTEx
rs28722697	RP11-114H24.2	cis	lung	GTEx
rs28722697	RP11-114H24.2	cis	Adipose Subcutaneous	GTEx
rs28722697	RP11-114H24.2	cis	Thyroid	GTEx
rs28722697	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs28722697	RP11-114H24.4	cis	Nerve Tibial	GTEx
rs28722697	RP11-114H24.2	cis	Esophagus Muscularis	GTEx
rs28722697	RP11-114H24.4	cis	Thyroid	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78236200-78237200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:78236200-78237200	Active TSS	Liver	Liver
3	chr15:78236200-78237400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:78236200-78237400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:78236200-78237400	Active TSS	Brain Angular Gyrus	brain
6	chr15:78236200-78237400	Active TSS	Brain Cingulate Gyrus	brain
7	chr15:78236200-78237400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:78236200-78237400	Active TSS	Rectal Smooth Muscle	rectum
9	chr15:78236200-78237400	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr15:78236200-78237400	Active TSS	NHDF-Ad	bronchial
11	chr15:78236200-78237600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:78236200-78237600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:78236200-78237600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:78236200-78237800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:78236400-78237200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:78236400-78237200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr15:78236400-78237200	Active TSS	Brain Anterior Caudate	brain
18	chr15:78236400-78237200	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr15:78236400-78237200	Active TSS	Colonic Mucosa	Colon
20	chr15:78236400-78237200	Active TSS	Colon Smooth Muscle	Colon
21	chr15:78236400-78237200	Active TSS	Pancreas	Pancrea
22	chr15:78236400-78237200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr15:78236400-78237200	Active TSS	HSMMtube	muscle
24	chr15:78236400-78237200	Active TSS	Osteobl	bone
25	chr15:78236400-78237400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:78236400-78237400	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr15:78236400-78237400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:78236400-78237400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:78236400-78237400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:78236400-78237400	Active TSS	Brain Germinal Matrix	brain
31	chr15:78236400-78237400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:78236400-78237400	Active TSS	Brain Substantia Nigra	brain
33	chr15:78236400-78237400	Active TSS	Fetal Brain Female	brain
34	chr15:78236400-78237400	Active TSS	Fetal Kidney	kidney
35	chr15:78236400-78237400	Active TSS	Ovary	ovary
36	chr15:78236400-78237400	Active TSS	Psoas Muscle	Psoas
37	chr15:78236400-78237400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr15:78236400-78237400	Active TSS	Right Ventricle	heart
39	chr15:78236400-78237400	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr15:78236400-78237600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr15:78236400-78237600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:78236400-78237600	Active TSS	Brain Hippocampus Middle	brain
43	chr15:78236400-78237600	Active TSS	Duodenum Mucosa	Duodenum
44	chr15:78236400-78237600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr15:78236600-78237200	Active TSS	H9 Cell Line	embryonic stem cell
46	chr15:78236600-78237200	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr15:78236600-78237200	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr15:78236600-78237200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:78236600-78237200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr15:78236600-78237200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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