Variant report

Variant	rs2857460
Chromosome Location	chr22:29664906-29664907
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	MXI1	chr22:29663380-29666062	GM12878	blood:	n/a	chr22:29664637-29664646 chr22:29664639-29664648
2	MXI1	chr22:29662695-29667112	IMR90	lung:	n/a	chr22:29664637-29664646 chr22:29664639-29664648
3	MAX	chr22:29663510-29664925	SK-N-SH	brain:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
4	POLR2A	chr22:29663541-29665184	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr22:29662422-29665050	GM12891	blood:	n/a	n/a
6	MYC	chr22:29663537-29665080	K562	blood:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
7	POLR2A	chr22:29663553-29665043	ECC-1	luminal epithelium:	n/a	n/a
8	YY1	chr22:29663566-29665082	GM12892	blood:	n/a	chr22:29664646-29664660 chr22:29664495-29664506 chr22:29664454-29664468 chr22:29664459-29664468 chr22:29665044-29665055
9	CHD1	chr22:29662615-29667443	IMR90	lung:	n/a	chr22:29664609-29664619
10	JUN	chr22:29663150-29665144	K562	blood:	n/a	n/a
11	CHD1	chr22:29663172-29665884	GM12878	blood:	n/a	chr22:29664609-29664619
12	POLR2A	chr22:29663160-29665372	GM15510	blood:	n/a	n/a
13	MAX	chr22:29663452-29664950	ECC-1	luminal epithelium:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
14	NFIC	chr22:29663672-29664940	GM12878	blood:	n/a	n/a
15	MAX	chr22:29663572-29665013	A549	lung:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
16	POLR2A	chr22:29663548-29665410	PFSK-1	brain:	n/a	n/a
17	TEAD4	chr22:29663629-29664946	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr22:29663602-29665023	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr22:29662634-29665656	K562	blood:	n/a	n/a
20	TAF1	chr22:29663551-29665027	SK-N-SH	brain:	n/a	n/a
21	MYC	chr22:29663611-29665080	H1-hESC	embryonic stem cell:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
22	POLR2A	chr22:29663637-29665012	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr22:29663212-29666867	Hela-S3	cervix:	n/a	n/a
24	YY1	chr22:29663558-29665128	HepG2	liver:	n/a	chr22:29664646-29664660 chr22:29664495-29664506 chr22:29664454-29664468 chr22:29664459-29664468 chr22:29665044-29665055
25	CHD2	chr22:29663335-29664934	K562	blood:	n/a	chr22:29664609-29664619
26	TAF1	chr22:29663553-29665025	ECC-1	luminal epithelium:	n/a	n/a
27	MYC	chr22:29663517-29665012	K562	blood:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
28	UBTF	chr22:29663061-29665015	K562	blood:	n/a	n/a
29	POLR2A	chr22:29661169-29667225	GM12878	blood:	n/a	n/a
30	MAX	chr22:29663507-29664980	GM12878	blood:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
31	POLR2A	chr22:29663042-29666706	GM12878	blood:	n/a	n/a
32	POLR2A	chr22:29662912-29664919	GM19099	blood:	n/a	n/a
33	SREBP1	chr22:29662829-29667473	GM12878	blood:	n/a	n/a
34	MAX	chr22:29663535-29665068	K562	blood:	n/a	chr22:29664640-29664649 chr22:29664638-29664647 chr22:29664638-29664647 chr22:29664637-29664648 chr22:29664638-29664647 chr22:29664638-29664648 chr22:29664643-29664653
35	WRNIP1	chr22:29662167-29666681	GM12878	blood:	n/a	n/a
36	CHD2	chr22:29663560-29665451	Hela-S3	cervix:	n/a	chr22:29664609-29664619
37	USF2	chr22:29663838-29664965	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr22:29662430-29667201	HepG2	liver:	n/a	n/a
39	POLR2A	chr22:29663516-29665148	HEK293	kidney:	n/a	n/a
40	STAT5A	chr22:29664648-29665536	GM12878	blood:	n/a	chr22:29665042-29665054
41	POLR2A	chr22:29663574-29664919	ECC-1	luminal epithelium:	n/a	n/a
42	HA-E2F1	chr22:29663482-29664923	MCF-7	breast:	n/a	chr22:29664647-29664657 chr22:29664249-29664258
43	POLR2A	chr22:29663124-29665194	HepG2	liver:	n/a	n/a
44	POLR2A	chr22:29663449-29666107	U87	brain:	n/a	n/a
45	REST	chr22:29663109-29665249	H1-neurons	neurons:	n/a	chr22:29664738-29664747
46	POLR2A	chr22:29664071-29665001	GM12891	blood:	n/a	n/a
47	POLR2A	chr22:29662999-29667217	GM12892	blood:	n/a	n/a
48	YY1	chr22:29663671-29664935	SK-N-SH_RA	brain:	n/a	chr22:29664646-29664660 chr22:29664495-29664506 chr22:29664454-29664468 chr22:29664459-29664468
49	POLR2A	chr22:29662846-29667160	GM12892	blood:	n/a	n/a
50	TAF1	chr22:29663551-29665140	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85741668..85742488-chr22:29664318..29665076,2	Hela-S3	cervix:
2	chr22:29661955..29666922-chr22:29700529..29704114,10	K562	blood:
3	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
4	chr22:29663275..29666008-chr22:29976454..29978804,2	K562	blood:
5	chr22:29194133..29196788-chr22:29662998..29665301,2	MCF-7	breast:
6	chr22:29663358..29665751-chr22:29702504..29704805,4	MCF-7	breast:
7	chr22:29663790..29666249-chr22:29704242..29708353,4	K562	blood:
8	chr11:62607720..62610465-chr22:29664145..29665718,2	MCF-7	breast:
9	chr22:29662577..29666963-chr22:29684296..29687849,8	MCF-7	breast:
10	chr22:29137011..29139217-chr22:29662922..29665353,2	MCF-7	breast:

Variant related genes	Relation type
RHBDD3	TF binding region
EWSR1	TF binding region
ENSG00000184117	Chromatin interaction
ENSG00000185340	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11702906	0.81[EUR][1000 genomes]
rs11703897	0.83[EUR][1000 genomes]
rs131184	1.00[ASN][1000 genomes]
rs131190	1.00[ASN][1000 genomes]
rs140064	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140065	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174760	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894414	0.90[EUR][1000 genomes]
rs2231398	0.93[ASN][1000 genomes]
rs2518683	0.83[ASN][1000 genomes]
rs2857464	0.87[EUR][1000 genomes]
rs5997460	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285200	0.81[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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29662400-29666000	Active TSS	Fetal Kidney	kidney
2	chr22:29662600-29665400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr22:29662600-29665800	Active TSS	Psoas Muscle	Psoas
4	chr22:29662800-29665200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr22:29662800-29665200	Active TSS	A549	lung
6	chr22:29662800-29665600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr22:29662800-29665600	Active TSS	GM12878-XiMat	blood
8	chr22:29662800-29666000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr22:29662800-29666400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:29662800-29666600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr22:29663000-29665400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr22:29663000-29665400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr22:29663000-29665400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr22:29663000-29665600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr22:29663000-29665800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr22:29663000-29666000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr22:29663000-29666000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr22:29663000-29666200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:29663000-29666400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr22:29663200-29665000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:29663200-29665000	Active TSS	NHEK	skin
22	chr22:29663200-29665200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr22:29663200-29665200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr22:29663200-29665200	Active TSS	K562	blood
25	chr22:29663200-29665200	Active TSS	NHDF-Ad	bronchial
26	chr22:29663200-29665400	Active TSS	Muscle Satellite Cultured Cells	--
27	chr22:29663200-29665400	Active TSS	Hela-S3	cervix
28	chr22:29663200-29665400	Bivalent/Poised TSS	HepG2	liver
29	chr22:29663200-29665800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:29663200-29665800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:29663200-29665800	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr22:29663200-29666000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:29663200-29666000	Active TSS	Small Intestine	intestine
34	chr22:29663200-29666000	Active TSS	HSMMtube	muscle
35	chr22:29663200-29666800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr22:29663200-29667000	Active TSS	Ovary	ovary
37	chr22:29663400-29665000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr22:29663400-29665000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr22:29663400-29665000	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr22:29663400-29665000	Active TSS	Dnd41	blood
41	chr22:29663400-29665200	Active TSS	Liver	Liver
42	chr22:29663400-29665200	Active TSS	Brain Angular Gyrus	brain
43	chr22:29663400-29665200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr22:29663400-29665200	Active TSS	Colonic Mucosa	Colon
45	chr22:29663400-29665200	Active TSS	Duodenum Mucosa	Duodenum
46	chr22:29663400-29665200	Active TSS	Placenta	Placenta
47	chr22:29663400-29665400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr22:29663400-29665400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:29663400-29665400	Active TSS	Brain Cingulate Gyrus	brain
50	chr22:29663400-29665400	Active TSS	Brain Hippocampus Middle	brain

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