Variant report

Variant	rs28516832
Chromosome Location	chr15:41367036-41367037
allele	A/G
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	chr15:41366926-41367174	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41366851..41369456-chr15:41474724..41476763,2	K562	blood:

Variant related genes	Relation type
INO80	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10851403	0.82[EUR][1000 genomes]
rs11852419	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855854	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	0.82[EUR][1000 genomes]
rs13329579	0.81[EUR][1000 genomes]
rs16971454	1.00[ASN][1000 genomes]
rs28382348	0.81[EUR][1000 genomes]
rs28493087	0.81[EUR][1000 genomes]
rs28538451	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551767	1.00[ASN][1000 genomes]
rs28827035	0.80[EUR][1000 genomes]
rs521890	0.81[EUR][1000 genomes]
rs522063	0.81[EUR][1000 genomes]
rs691011	0.81[EUR][1000 genomes]
rs691629	0.81[EUR][1000 genomes]
rs691906	0.81[EUR][1000 genomes]
rs691907	0.81[EUR][1000 genomes]
rs8038983	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv974711	chr15:41360002-41370961	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28516832	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28516832	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28516832	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28516832	NDUFAF1	cis	multi-tissue	Pritchard
rs28516832	NDUFAF1	cis	Thyroid	GTEx
rs28516832	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28516832	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28516832	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28516832	NDUFAF1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:41336800-41380400	Strong transcription	Osteobl	bone
4	chr15:41341600-41389000	Strong transcription	Liver	Liver
5	chr15:41345200-41373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41346800-41368600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:41347000-41380200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:41354000-41368600	Strong transcription	NH-A	brain
9	chr15:41354200-41389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:41354600-41367400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr15:41354600-41388800	Strong transcription	Fetal Intestine Large	intestine
12	chr15:41354600-41389000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr15:41354800-41388600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr15:41354800-41389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:41355000-41367200	Strong transcription	Ovary	ovary
16	chr15:41355000-41367400	Strong transcription	Adipose Nuclei	Adipose
17	chr15:41355000-41369200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:41355000-41370800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr15:41355000-41374200	Strong transcription	Hela-S3	cervix
20	chr15:41355000-41380200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:41355000-41380800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:41355000-41381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:41355000-41388400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
25	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
26	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:41355200-41367200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:41355200-41370600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:41355200-41388600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:41355200-41388800	Strong transcription	Primary T cells from cord blood	blood
32	chr15:41355400-41368800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:41355400-41369000	Strong transcription	Thymus	Thymus
34	chr15:41355400-41369200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:41355400-41370800	Weak transcription	Pancreas	Pancrea
36	chr15:41355400-41371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:41355400-41378400	Strong transcription	Fetal Muscle Leg	muscle
38	chr15:41355400-41383200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:41355400-41388800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:41355400-41389200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:41355400-41390200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41355600-41370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:41355600-41390800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:41355800-41367200	Strong transcription	NHEK	skin
46	chr15:41355800-41370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:41355800-41381800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:41355800-41389200	Strong transcription	Dnd41	blood
49	chr15:41355800-41391000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:41356000-41367400	Strong transcription	H1 Cell Line	embryonic stem cell

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