Variant report

Variant	rs4886456
Chromosome Location	chr15:76015867-76015868
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	SMARCC1	chr15:76015634-76016770	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr15:76015405-76017112	IMR90	lung:	n/a	chr15:76016000-76016010 chr15:76016278-76016287
3	POLR2A	chr15:76015719-76016620	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr15:76015568-76016560	IMR90	lung:	n/a	chr15:76016272-76016287 chr15:76016274-76016289
5	RCOR1	chr15:76015817-76015938	GM12878	blood:	n/a	n/a
6	ZNF263	chr15:76015508-76016473	HEK293-T-REx	kidney:	n/a	chr15:76015785-76015806 chr15:76015885-76015894
7	JUN	chr15:76015341-76016687	K562	blood:	n/a	chr15:76016330-76016343 chr15:76016331-76016340
8	POLR2A	chr15:76015686-76017007	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ODF3L1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10467951	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851883	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs12594714	0.96[CEU][hapmap]
rs12908447	0.96[CEU][hapmap]
rs2255254	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255269	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405895	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405897	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2405898	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2405902	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2593286	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593293	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593298	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2604411	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2675216	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2675217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675220	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886458	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886735	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886953	0.86[EUR][1000 genomes]
rs749161	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023610	0.82[EUR][1000 genomes]
rs8032669	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
6	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886456	NRG4	cis	parietal	SCAN
rs4886456	ETFA	cis	parietal	SCAN
rs4886456	NRG4	cis	cerebellum	SCAN
rs4886456	TRAPPC9	trans	parietal	SCAN
rs4886456	C15orf59	cis	parietal	SCAN
rs4886456	ARID3B	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76005600-76016000	Weak transcription	Aorta	Aorta
2	chr15:76008200-76016000	Weak transcription	Gastric	stomach
3	chr15:76009400-76017600	Enhancers	Stomach Mucosa	stomach
4	chr15:76011200-76016000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:76011400-76016000	Weak transcription	HSMMtube	muscle
6	chr15:76011600-76016000	Weak transcription	Ovary	ovary
7	chr15:76011600-76016000	Weak transcription	NHDF-Ad	bronchial
8	chr15:76013000-76018600	Enhancers	Fetal Muscle Leg	muscle
9	chr15:76013200-76016000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr15:76013200-76017800	Enhancers	Fetal Stomach	stomach
11	chr15:76013400-76017200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:76013600-76016000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:76013600-76025000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:76013800-76016000	Weak transcription	Liver	Liver
15	chr15:76013800-76016000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:76013800-76016000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:76013800-76016000	Weak transcription	GM12878-XiMat	blood
18	chr15:76013800-76029800	Weak transcription	HSMM	muscle
19	chr15:76014000-76016000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:76014000-76016000	Weak transcription	Brain Angular Gyrus	brain
21	chr15:76014200-76018800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr15:76014800-76016000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:76014800-76017600	Enhancers	Fetal Intestine Small	intestine
24	chr15:76015000-76016000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:76015000-76017000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:76015000-76017000	Enhancers	Fetal Thymus	thymus
27	chr15:76015200-76016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:76015200-76016000	Weak transcription	Spleen	Spleen
29	chr15:76015200-76016600	Enhancers	A549	lung
30	chr15:76015200-76016800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:76015200-76017000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr15:76015200-76017000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr15:76015200-76017200	Enhancers	Colon Smooth Muscle	Colon
34	chr15:76015200-76017200	Enhancers	Fetal Lung	lung
35	chr15:76015200-76017600	Enhancers	Fetal Intestine Large	intestine
36	chr15:76015400-76016200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:76015400-76016600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr15:76015400-76018600	Enhancers	Placenta	Placenta
39	chr15:76015600-76016000	Enhancers	HepG2	liver
40	chr15:76015600-76016600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:76015600-76016600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:76015600-76016600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr15:76015600-76016600	Enhancers	Brain Germinal Matrix	brain
44	chr15:76015600-76016600	Enhancers	Esophagus	oesophagus
45	chr15:76015600-76016600	Enhancers	Left Ventricle	heart
46	chr15:76015600-76016600	Enhancers	Lung	lung
47	chr15:76015600-76016600	Enhancers	Small Intestine	intestine
48	chr15:76015600-76016600	Enhancers	K562	blood
49	chr15:76015600-76016800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:76015600-76016800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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