Variant report

Variant	rs28575174
Chromosome Location	chr15:41244944-41244945
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	SP4	chr15:41244862-41246065	H1-hESC	embryonic stem cell:	n/a	chr15:41246045-41246061 chr15:41245611-41245627
2	RFX5	chr15:41244826-41246079	SK-N-SH	brain:	n/a	chr15:41245500-41245509
3	MAX	chr15:41244849-41246050	A549	lung:	n/a	chr15:41245041-41245050
4	MYC	chr15:41244811-41245706	H1-hESC	embryonic stem cell:	n/a	chr15:41245041-41245050
5	GTF2F1	chr15:41244675-41245972	Hela-S3	cervix:	n/a	n/a
6	REST	chr15:41244829-41246248	H1-neurons	neurons:	n/a	chr15:41245517-41245530 chr15:41245604-41245617 chr15:41245601-41245614
7	POLR2A	chr15:41244087-41246309	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:41244687-41246812	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXP2	chr15:41244864-41246113	PFSK-1	brain:	n/a	n/a
10	TAF7	chr15:41244820-41245496	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr15:41244676-41246153	H1-hESC	embryonic stem cell:	n/a	chr15:41245560-41245569 chr15:41244988-41244998 chr15:41245126-41245133 chr15:41245126-41245133 chr15:41245336-41245346 chr15:41245126-41245133
12	RFX5	chr15:41244745-41245828	Hela-S3	cervix:	n/a	chr15:41245500-41245509
13	MAZ	chr15:41244802-41245909	K562	blood:	n/a	chr15:41245041-41245050
14	POLR2A	chr15:41244901-41245868	A549	lung:	n/a	n/a
15	POLR2A	chr15:41244822-41246504	PBDE	blood:	n/a	n/a
16	POLR2A	chr15:41244697-41246315	GM19193	blood:	n/a	n/a
17	POLR2A	chr15:41244452-41246039	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr15:41244700-41245945	MCF-7	breast:	n/a	n/a
19	POLR2A	chr15:41244823-41245521	A549	lung:	n/a	n/a
20	SMARCC1	chr15:41244649-41246206	Hela-S3	cervix:	n/a	n/a
21	TBP	chr15:41244635-41246113	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr15:41244826-41245720	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr15:41244823-41245962	H1-hESC	embryonic stem cell:	n/a	chr15:41245339-41245350
24	MAX	chr15:41244754-41245921	H1-hESC	embryonic stem cell:	n/a	chr15:41245041-41245050
25	POLR2A	chr15:41244732-41246033	U87	brain:	n/a	n/a
26	TEAD4	chr15:41244842-41245287	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr15:41244660-41246865	PFSK-1	brain:	n/a	n/a
28	CEBPB	chr15:41244938-41245830	A549	lung:	n/a	n/a
29	CEBPB	chr15:41244867-41245996	HCT-116	colon:	n/a	n/a
30	SMARCB1	chr15:41244539-41246091	Hela-S3	cervix:	n/a	n/a
31	MAZ	chr15:41244832-41246688	IMR90	lung:	n/a	chr15:41245041-41245050
32	POLR2A	chr15:41244905-41246099	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr15:41244897-41246577	GM18505	blood:	n/a	n/a
34	TAF7	chr15:41244765-41246828	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr15:41244495-41246332	GM12892	blood:	n/a	n/a
36	MYC	chr15:41244911-41245898	K562	blood:	n/a	chr15:41245041-41245050
37	POLR2A	chr15:41244585-41246933	H1-hESC	embryonic stem cell:	n/a	n/a
38	E2F6	chr15:41244803-41245986	H1-hESC	embryonic stem cell:	n/a	chr15:41245560-41245569 chr15:41244988-41244998 chr15:41245126-41245133 chr15:41245126-41245133 chr15:41245336-41245346 chr15:41245126-41245133
39	POLR2A	chr15:41244621-41246297	MCF-7	breast:	n/a	n/a
40	POLR2A	chr15:41244452-41246146	HCT-116	colon:	n/a	n/a
41	POLR2A	chr15:41244884-41245985	HL-60	blood:	n/a	n/a
42	GTF2F1	chr15:41244620-41245810	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr15:41244764-41246290	HCT-116	colon:	n/a	n/a
44	YY1	chr15:41244923-41245748	K562	blood:	n/a	chr15:41245339-41245350
45	ZBTB7A	chr15:41244783-41246145	ECC-1	luminal epithelium:	n/a	n/a
46	SIN3A	chr15:41244716-41246763	H1-hESC	embryonic stem cell:	n/a	chr15:41245601-41245614
47	MXI1	chr15:41244726-41246877	IMR90	lung:	n/a	n/a
48	TAF1	chr15:41244759-41246291	ECC-1	luminal epithelium:	n/a	n/a
49	CHD1	chr15:41244703-41245305	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr15:41244773-41245543	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41243575..41247241-chr15:41275161..41277167,3	MCF-7	breast:
2	chr15:41219948..41223850-chr15:41241031..41249080,13	K562	blood:
3	chr15:41196932..41200984-chr15:41244050..41248455,6	K562	blood:
4	chr15:41244727..41245305-chr9:91933111..91933989,2	Hela-S3	cervix:
5	chr15:41046641..41048842-chr15:41243931..41246219,2	K562	blood:
6	chr15:41219573..41224863-chr15:41243808..41249661,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC1-1	chr15:41244582-41245400	XLOC_011224

Variant related genes	Relation type
ISCA1P4	TF binding region
CHAC1	TF binding region
ENSG00000128917	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10851400	0.98[ASN][1000 genomes]
rs11070313	0.93[ASN][1000 genomes]
rs11070314	0.94[ASN][1000 genomes]
rs11557249	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634736	0.91[EUR][1000 genomes]
rs11853377	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854054	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11857572	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593739	0.90[ASN][1000 genomes]
rs4924520	0.93[ASN][1000 genomes]
rs60588038	0.94[ASN][1000 genomes]
rs7174555	0.91[ASN][1000 genomes]
rs7175269	0.91[EUR][1000 genomes]
rs745299	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042127	0.84[ASN][1000 genomes]
rs8042230	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28575174	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41244000-41245200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:41244200-41246200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:41244400-41245000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
4	chr15:41244400-41245000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:41244400-41245000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:41244400-41245000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:41244400-41245000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:41244400-41245000	Flanking Active TSS	Stomach Mucosa	stomach
9	chr15:41244400-41245000	Enhancers	Spleen	Spleen
10	chr15:41244400-41245200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr15:41244400-41245200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr15:41244400-41245200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr15:41244400-41245200	Flanking Active TSS	Dnd41	blood
14	chr15:41244400-41245200	Flanking Active TSS	GM12878-XiMat	blood
15	chr15:41244400-41245200	Flanking Active TSS	Hela-S3	cervix
16	chr15:41244400-41245200	Flanking Active TSS	K562	blood
17	chr15:41244400-41245200	Flanking Active TSS	NHEK	skin
18	chr15:41244400-41245400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:41244400-41245400	Flanking Active TSS	Pancreas	Pancrea
20	chr15:41244400-41245400	Flanking Active TSS	HMEC	breast
21	chr15:41244400-41246200	Active TSS	A549	lung
22	chr15:41244400-41246600	Active TSS	Brain Angular Gyrus	brain
23	chr15:41244400-41246800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:41244400-41246800	Active TSS	Rectal Smooth Muscle	rectum
25	chr15:41244600-41245000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:41244600-41245000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:41244600-41245000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr15:41244600-41245000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:41244600-41245000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr15:41244600-41245200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:41244600-41245200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr15:41244600-41245200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr15:41244600-41245200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr15:41244600-41245200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:41244600-41245200	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr15:41244600-41245200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr15:41244600-41245200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr15:41244600-41245400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:41244600-41245600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:41244600-41246000	Enhancers	Fetal Brain Male	brain
41	chr15:41244600-41246000	Active TSS	Osteobl	bone
42	chr15:41244600-41246200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:41244600-41246200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr15:41244600-41246200	Active TSS	HSMM	muscle
45	chr15:41244600-41246200	Active TSS	NHLF	lung
46	chr15:41244600-41246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:41244600-41246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:41244600-41246400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:41244600-41246400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr15:41244600-41246400	Flanking Active TSS	Liver	Liver

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