Variant report

Variant	rs2922231
Chromosome Location	chr15:57848578-57848579
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	CTCF	chr15:57848440-57848590	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000240874	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11856	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439291	0.86[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs12439292	0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1620315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1620402	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs1623697	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs1626448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1666572	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1666573	0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1690316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820431	0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs17820437	0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs17820449	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17820461	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17820467	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1908189	0.95[ASN][1000 genomes]
rs1908191	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908192	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131730	0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131731	0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270487	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635389	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2922232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934418	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3742963	0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs3742964	0.85[AMR][1000 genomes]
rs4774960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4774961	0.81[EUR][1000 genomes]
rs4774962	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55916627	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55952634	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56362917	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59368768	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66802357	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67336499	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7166305	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7171354	0.87[EUR][1000 genomes]
rs7171360	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72741528	0.80[EUR][1000 genomes]
rs8038795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937248	0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9744909	0.81[AFR][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv984075	chr15:57848182-57848879	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2922231	CCNB2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
3	chr15:57841000-57848600	Enhancers	HSMMtube	muscle
4	chr15:57842800-57848600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:57843000-57848600	Enhancers	Fetal Lung	lung
6	chr15:57844200-57848800	Enhancers	Fetal Heart	heart
7	chr15:57844600-57852200	Weak transcription	HepG2	liver
8	chr15:57844600-57859000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:57844800-57848600	Enhancers	Hela-S3	cervix
10	chr15:57844800-57857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:57845200-57852400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:57845200-57857600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:57845400-57848600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:57846200-57852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:57846800-57861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:57847000-57854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:57847200-57853400	Weak transcription	NHEK	skin
18	chr15:57847200-57854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:57847400-57848600	Enhancers	Psoas Muscle	Psoas
20	chr15:57847400-57852200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:57847600-57849000	Enhancers	HUVEC	blood vessel
22	chr15:57847600-57851800	Weak transcription	Liver	Liver
23	chr15:57847600-57852200	Weak transcription	A549	lung
24	chr15:57847600-57852200	Weak transcription	HMEC	breast
25	chr15:57847600-57853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:57847600-57854400	Weak transcription	Pancreas	Pancrea
27	chr15:57847600-57859200	Weak transcription	Right Ventricle	heart
28	chr15:57847800-57848600	Weak transcription	Brain Anterior Caudate	brain
29	chr15:57847800-57850200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:57847800-57852000	Weak transcription	Stomach Mucosa	stomach
31	chr15:57847800-57852400	Weak transcription	Fetal Intestine Large	intestine
32	chr15:57847800-57852400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:57847800-57852600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:57847800-57853600	Weak transcription	Fetal Stomach	stomach
35	chr15:57847800-57859000	Weak transcription	Gastric	stomach
36	chr15:57847800-57859200	Weak transcription	Ovary	ovary
37	chr15:57847800-57859200	Weak transcription	Right Atrium	heart
38	chr15:57848000-57852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:57848200-57848800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:57848200-57849400	Enhancers	Fetal Muscle Trunk	muscle
41	chr15:57848200-57851000	Weak transcription	NH-A	brain

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