Variant report

Variant	rs28503916
Chromosome Location	chr15:41698296-41698297
allele	C/T
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	POLR2A	chr15:41697962-41698335	HepG2	liver:	n/a	n/a
2	CEBPB	chr15:41698185-41698316	K562	blood:	n/a	chr15:41698220-41698231

No.	Distal block	Cell Line	Cell type
1	chr15:41696803..41699662-chr15:41700695..41704414,5	MCF-7	breast:
2	chr15:41696720..41701906-chr15:41705029..41710558,10	MCF-7	breast:
3	chr15:41693181..41695675-chr15:41697885..41700748,3	MCF-7	breast:

Variant related genes	Relation type
RTF1	TF binding region
NDUFAF1	TF binding region
ENSG00000137806	Chromatin interaction
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28479336	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28508151	1.00[ASN][1000 genomes]
rs28631111	1.00[ASN][1000 genomes]
rs28662502	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924549	1.00[ASN][1000 genomes]
rs72739663	1.00[AFR][1000 genomes];1.00[ASN][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	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv569232	chr15:41694377-41730246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28503916	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28503916	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28503916	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28503916	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41695000-41700200	Weak transcription	Fetal Brain Male	brain
2	chr15:41695400-41700400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:41695400-41700400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:41695400-41700400	Weak transcription	Ovary	ovary
5	chr15:41695400-41700400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:41695400-41703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:41695400-41707800	Weak transcription	HSMMtube	muscle
8	chr15:41695400-41708400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:41695600-41699600	Weak transcription	Fetal Intestine Large	intestine
10	chr15:41695600-41699800	Weak transcription	Fetal Intestine Small	intestine
11	chr15:41695600-41700200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:41695600-41700200	Weak transcription	Placenta	Placenta
13	chr15:41695600-41700400	Weak transcription	Psoas Muscle	Psoas
14	chr15:41695600-41700400	Weak transcription	NHEK	skin
15	chr15:41695600-41701800	Weak transcription	K562	blood
16	chr15:41695600-41707600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:41695600-41707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:41695600-41708400	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:41695800-41700400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:41696000-41699200	Enhancers	Primary B cells from cord blood	blood
21	chr15:41696000-41700400	Weak transcription	Pancreas	Pancrea
22	chr15:41696000-41700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:41696000-41701600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41696000-41701800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:41696200-41700400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:41696200-41700400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:41697000-41699200	Weak transcription	HepG2	liver
28	chr15:41697400-41700200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:41697400-41707800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:41697600-41699400	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr15:41698000-41699200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr15:41698200-41699600	Weak transcription	Monocytes-CD14+_RO01746	blood

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