Variant report

Variant	rs2688240
Chromosome Location	chr4:8508231-8508232
allele	G/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	BACH1	chr4:8508063-8508360	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr4:8507872-8508585	H1-hESC	embryonic stem cell:	n/a	chr4:8508449-8508458 chr4:8507956-8507966 chr4:8507958-8507968 chr4:8507957-8507968 chr4:8507960-8507976 chr4:8507958-8507967 chr4:8507959-8507966
3	ZNF143	chr4:8508107-8508422	H1-hESC	embryonic stem cell:	n/a	chr4:8508173-8508191
4	GTF2F1	chr4:8508186-8508270	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:8508100-8508250	HAc	cerebellar:	n/a	chr4:8508168-8508181
6	JUND	chr4:8508025-8508245	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr4:8508120-8508270	HCPEpiC	choroid plexus:	n/a	chr4:8508168-8508181
8	TEAD4	chr4:8507952-8508531	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:8508200-8508350	AoAF	blood vessel:	n/a	n/a
10	GABPA	chr4:8508026-8508363	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr4:8507937-8508491	H1-hESC	embryonic stem cell:	n/a	chr4:8508305-8508319
12	MXI1	chr4:8508196-8509158	IMR90	lung:	n/a	n/a
13	RXRA	chr4:8508041-8508473	H1-hESC	embryonic stem cell:	n/a	n/a
14	RXRA	chr4:8508062-8508475	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:8507701-8508402	K562	blood:	n/a	n/a
16	CHD2	chr4:8507994-8508447	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr4:8507904-8508347	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYC	chr4:8507950-8508232	H1-hESC	embryonic stem cell:	n/a	chr4:8507956-8507966 chr4:8507958-8507968 chr4:8507957-8507968 chr4:8507960-8507976 chr4:8507958-8507967 chr4:8507959-8507966
19	CTCF	chr4:8508100-8508250	BJ	skin:	n/a	chr4:8508168-8508181
20	TEAD4	chr4:8507992-8508593	H1-hESC	embryonic stem cell:	n/a	n/a
21	RCOR1	chr4:8508093-8509345	IMR90	lung:	n/a	n/a
22	MAX	chr4:8507926-8508334	H1-hESC	embryonic stem cell:	n/a	chr4:8507956-8507966 chr4:8507958-8507968 chr4:8507957-8507968 chr4:8507960-8507976 chr4:8507958-8507967 chr4:8507959-8507966
23	RAD21	chr4:8507766-8508439	H1-hESC	embryonic stem cell:	n/a	chr4:8508416-8508430

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8506167..8508857-chr4:8582205..8583898,2	MCF-7	breast:
2	chr4:8507896..8508408-chr4:8595816..8596778,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205959	TF binding region
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11722806	0.81[JPT][hapmap]
rs11729265	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12503034	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1880025	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2002860	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2140336	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2245515	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2245808	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2386223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2631723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631724	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631727	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631728	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2631729	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631730	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2631733	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631737	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2631757	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631763	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2631764	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631765	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2631766	0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2631767	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2631769	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688221	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2688228	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2688229	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2688230	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2688234	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688239	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3103090	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3103098	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3115396	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775893	0.81[EUR][1000 genomes]
rs4325994	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56343159	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs954270	0.89[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs954271	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[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	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3327752	chr4:8507302-8509800	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2688240	ACOX3	cis	lymphoblastoid	seeQTL
rs2688240	RP11-774O3.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8501800-8510600	Enhancers	Ovary	ovary
2	chr4:8502800-8512800	Enhancers	Placenta	Placenta
3	chr4:8503600-8509400	Enhancers	Right Ventricle	heart
4	chr4:8503600-8509800	Enhancers	Adipose Nuclei	Adipose
5	chr4:8504200-8509000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr4:8504200-8509400	Enhancers	Right Atrium	heart
7	chr4:8504200-8510600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:8504600-8510800	Enhancers	Fetal Muscle Leg	muscle
9	chr4:8505400-8509000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:8505800-8509600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:8505800-8509800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:8506000-8509000	Enhancers	Spleen	Spleen
13	chr4:8506200-8509600	Enhancers	HSMMtube	muscle
14	chr4:8506400-8509200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:8506600-8508600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:8507000-8509200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:8507000-8509800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr4:8507200-8509400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:8507200-8509400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:8507200-8512000	Weak transcription	Gastric	stomach
21	chr4:8507400-8509200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:8507400-8509400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:8507400-8509400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:8507400-8509400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:8507600-8508800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:8507600-8508800	Enhancers	Fetal Brain Male	brain
27	chr4:8507600-8509000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:8507600-8509400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr4:8507600-8509400	Enhancers	Fetal Lung	lung
30	chr4:8507600-8509600	Enhancers	Colon Smooth Muscle	Colon
31	chr4:8507800-8508800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:8507800-8508800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:8507800-8508800	Enhancers	Fetal Stomach	stomach
34	chr4:8507800-8509000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr4:8507800-8509000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:8507800-8509200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:8507800-8509200	Enhancers	Aorta	Aorta
38	chr4:8507800-8509200	Enhancers	Brain Hippocampus Middle	brain
39	chr4:8507800-8509200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:8507800-8509200	Enhancers	Brain Substantia Nigra	brain
41	chr4:8507800-8509200	Enhancers	Colonic Mucosa	Colon
42	chr4:8507800-8509200	Enhancers	Left Ventricle	heart
43	chr4:8507800-8509200	Enhancers	NH-A	brain
44	chr4:8507800-8509400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:8507800-8509400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:8507800-8509400	Enhancers	Brain Angular Gyrus	brain
47	chr4:8507800-8509400	Enhancers	Brain Anterior Caudate	brain
48	chr4:8507800-8509400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:8507800-8509600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:8507800-8509600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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