Variant report

Variant	rs130456
Chromosome Location	chr22:32925170-32925171
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	CTCF	chr22:32924900-32925267	NHEK	skin:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
2	CTCF	chr22:32924909-32925317	K562	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
3	MXI1	chr22:32925014-32925282	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr22:32925002-32925208	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr22:32924942-32925250	GM12878	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
6	RFX5	chr22:32924963-32925434	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr22:32924850-32925333	IMR90	lung:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
8	MYBL2	chr22:32924912-32925583	HepG2	liver:	n/a	n/a
9	CTCF	chr22:32925040-32925190	GM12874	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
10	RAD21	chr22:32924907-32925278	K562	blood:	n/a	chr22:32925096-32925115
11	MYC	chr22:32925016-32925254	K562	blood:	n/a	n/a
12	CTCF	chr22:32925020-32925170	MCF-7	breast:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
13	CTCF	chr22:32924864-32925307	GM12878	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
14	CTCF	chr22:32924942-32925219	GM10266	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
15	CTCF	chr22:32925020-32925170	BJ	skin:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
16	CTCF	chr22:32925040-32925190	AG10803	skin:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
17	CTCF	chr22:32925060-32925210	GM12870	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
18	RAD21	chr22:32924851-32925316	SK-N-SH_RA	brain:	n/a	chr22:32925096-32925115
19	CTCF	chr22:32925040-32925190	GM12872	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
20	RAD21	chr22:32924776-32925648	Hela-S3	cervix:	n/a	chr22:32925096-32925115
21	CTCF	chr22:32925020-32925170	HVMF	connective:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
22	RAD21	chr22:32924690-32925470	HCT-116	colon:	n/a	chr22:32925096-32925115
23	YY1	chr22:32924820-32925365	HepG2	liver:	n/a	n/a
24	RCOR1	chr22:32925025-32925412	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr22:32924847-32925289	A549	lung:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
26	SMC3	chr22:32924899-32925317	GM12878	blood:	n/a	chr22:32925097-32925111
27	RAD21	chr22:32924859-32925229	H1-hESC	embryonic stem cell:	n/a	chr22:32925096-32925115
28	CTCF	chr22:32925040-32925190	RPTEC	kidney:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
29	SMC3	chr22:32924831-32925550	HepG2	liver:	n/a	chr22:32925097-32925111
30	CTCF	chr22:32925020-32925170	BE2_C	brain:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
31	CTCF	chr22:32924954-32925243	Kidney_OC	kidney:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
32	CTCF	chr22:32925020-32925170	AoAF	blood vessel:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
33	CHD2	chr22:32924982-32925228	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr22:32924977-32925315	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr22:32924888-32925250	SK-N-SH_RA	brain:	n/a	chr22:32925096-32925115
36	CEBPB	chr22:32925049-32925244	H1-hESC	embryonic stem cell:	n/a	n/a
37	GABPA	chr22:32924897-32925221	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr22:32925019-32925263	A549	lung:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
39	CHD2	chr22:32924936-32925340	Hela-S3	cervix:	n/a	n/a
40	EP300	chr22:32924932-32925581	HepG2	liver:	n/a	n/a
41	WRNIP1	chr22:32924970-32925175	GM12878	blood:	n/a	n/a
42	JUND	chr22:32925032-32925382	K562	blood:	n/a	n/a
43	CTCF	chr22:32924932-32925249	GM19239	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
44	RAD21	chr22:32924848-32925315	ECC-1	luminal epithelium:	n/a	chr22:32925096-32925115
45	CTCF	chr22:32925040-32925190	NB4	blood:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
46	MAZ	chr22:32924682-32925960	IMR90	lung:	n/a	n/a
47	CTCF	chr22:32925040-32925190	SK-N-SH_RA	brain:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
48	CTCF	chr22:32925020-32925170	HCM	heart:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112
49	EP300	chr22:32924991-32925607	HepG2	liver:	n/a	n/a
50	CTCF	chr22:32924951-32925396	MCF-7	breast:	n/a	chr22:32925095-32925113 chr22:32925100-32925110 chr22:32925097-32925118 chr22:32925096-32925112

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32920308-32927723..22:33178968-33185617	Hela-S3	cervix:
2	22:32920308-32927723..22:33389304-33403028	K562	blood:
3	22:32920308-32927723..22:33208968-33216036	H1-hESC	embryonic stem cell:	embryo
4	chr22:32922025..32930472-chr22:33196157..33204507,15	MCF-7	breast:
5	22:32920308-32927723..22:33253287-33262063	Hela-S3	cervix:

Variant related genes	Relation type
SYN3	TF binding region
ENSG00000229673	Chromatin interaction
ENSG00000197047	Chromatin interaction
ENSG00000100234	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000183531	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs130451	0.80[EUR][1000 genomes]
rs130452	0.81[EUR][1000 genomes]
rs130457	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs135123	0.80[EUR][1000 genomes]
rs135479	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs2710380	1.00[CEU][hapmap]
rs2858335	0.80[CEU][hapmap]
rs2858337	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs4550760	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs5754144	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs762908	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914981	chr22:32912277-32940660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs130456	RNF185	cis	parietal	SCAN
rs130456	SEC14L2	cis	parietal	SCAN
rs130456	AP1B1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32898600-32928000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:32898800-32927200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:32910200-32925600	Weak transcription	Spleen	Spleen
4	chr22:32914200-32928000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr22:32914400-32928200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr22:32914400-32932000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:32916000-32927600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr22:32920200-32928000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr22:32923600-32931400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:32923800-32925400	Enhancers	K562	blood
11	chr22:32923800-32926400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr22:32924000-32925200	Active TSS	Brain Anterior Caudate	brain
13	chr22:32924200-32925200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr22:32924200-32925400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:32924200-32932200	Enhancers	Placenta	Placenta
16	chr22:32924400-32925200	Active TSS	Brain Angular Gyrus	brain
17	chr22:32924400-32925200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr22:32924400-32925400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:32924400-32926200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:32924400-32926200	Enhancers	Right Ventricle	heart
21	chr22:32924400-32930200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:32924600-32925200	Active TSS	Brain Substantia Nigra	brain
23	chr22:32924600-32925400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr22:32924600-32925400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr22:32924600-32932000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr22:32924600-32932800	Enhancers	Fetal Muscle Leg	muscle
27	chr22:32924800-32925200	Active TSS	Colon Smooth Muscle	Colon
28	chr22:32924800-32925200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr22:32924800-32925600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:32924800-32925800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:32924800-32925800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:32924800-32925800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:32924800-32926000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:32924800-32926000	Enhancers	Ovary	ovary
35	chr22:32924800-32926200	Enhancers	Lung	lung
36	chr22:32924800-32926400	Enhancers	Duodenum Mucosa	Duodenum
37	chr22:32924800-32926400	Enhancers	Left Ventricle	heart
38	chr22:32924800-32926600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr22:32924800-32928000	Enhancers	Adipose Nuclei	Adipose
40	chr22:32924800-32931000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr22:32924800-32931200	Enhancers	Fetal Lung	lung
42	chr22:32924800-32931200	Enhancers	NHDF-Ad	bronchial
43	chr22:32924800-32932200	Enhancers	Fetal Stomach	stomach
44	chr22:32925000-32925200	Active TSS	Brain Cingulate Gyrus	brain
45	chr22:32925000-32925200	Enhancers	Brain Hippocampus Middle	brain
46	chr22:32925000-32925200	Enhancers	Hela-S3	cervix
47	chr22:32925000-32925400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:32925000-32925400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr22:32925000-32925400	Active TSS	HepG2	liver
50	chr22:32925000-32925600	Enhancers	Osteobl	bone

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