Variant report

Variant	rs3747093
Chromosome Location	chr22:21984379-21984380
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	TBP	chr22:21983562-21984506	HepG2	liver:	n/a	n/a
2	MYC	chr22:21984063-21984530	MCF-7	breast:	n/a	n/a
3	MAZ	chr22:21983496-21984569	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:21982760-21984539	NB4	blood:	n/a	n/a
5	HMGN3	chr22:21982380-21984639	K562	blood:	n/a	n/a
6	USF2	chr22:21983312-21984585	K562	blood:	n/a	chr22:21984395-21984411
7	MAX	chr22:21983312-21984595	GM12878	blood:	n/a	n/a
8	BACH1	chr22:21983243-21984544	K562	blood:	n/a	n/a
9	POLR2A	chr22:21980580-21984939	K562	blood:	n/a	n/a
10	RUNX3	chr22:21983152-21984635	GM12878	blood:	n/a	n/a
11	MAZ	chr22:21983386-21984586	GM12878	blood:	n/a	n/a
12	E2F6	chr22:21982481-21984627	K562	blood:	n/a	chr22:21983082-21983094
13	POLR2A	chr22:21982968-21984511	MCF10A-Er-Src	breast:	n/a	n/a
14	MTA3	chr22:21983084-21984523	GM12878	blood:	n/a	n/a
15	CTCF	chr22:21984208-21984611	MCF-7	breast:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
16	CTCF	chr22:21984357-21984539	HepG2	liver:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
17	CTCF	chr22:21982333-21984660	K562	blood:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
18	CTCF	chr22:21982359-21984783	K562	blood:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
19	POLR2A	chr22:21984056-21984543	GM12891	blood:	n/a	n/a
20	POLR2A	chr22:21982137-21984611	GM18505	blood:	n/a	n/a
21	GABPA	chr22:21983191-21984602	K562	blood:	n/a	n/a
22	SMC3	chr22:21984139-21984631	Hela-S3	cervix:	n/a	chr22:21984431-21984445
23	CTCF	chr22:21984317-21984612	ECC-1	luminal epithelium:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
24	CTCF	chr22:21984360-21984510	GM12875	blood:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
25	CTBP2	chr22:21983512-21984602	H1-hESC	embryonic stem cell:	n/a	n/a
26	TAF1	chr22:21983540-21984536	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr22:21983160-21984507	A549	lung:	n/a	n/a
28	NRF1	chr22:21984115-21984476	H1-hESC	embryonic stem cell:	n/a	chr22:21984282-21984293
29	TAF1	chr22:21984113-21984379	GM12892	blood:	n/a	n/a
30	CTCF	chr22:21984320-21984470	WI-38	lung:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
31	ELF1	chr22:21982929-21984644	HCT-116	colon:	n/a	chr22:21983202-21983211 chr22:21983202-21983213 chr22:21983178-21983187 chr22:21983203-21983212 chr22:21983202-21983213
32	POLR2A	chr22:21983341-21984566	PFSK-1	brain:	n/a	n/a
33	RCOR1	chr22:21983594-21984557	HepG2	liver:	n/a	n/a
34	CTCF	chr22:21983061-21984772	SK-N-SH	brain:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
35	MAX	chr22:21983179-21984580	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr22:21984310-21984584	Medullo	brain:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
37	MAZ	chr22:21983324-21984600	IMR90	lung:	n/a	n/a
38	POLR2A	chr22:21983233-21984466	A549	lung:	n/a	n/a
39	MAX	chr22:21983374-21984595	H1-hESC	embryonic stem cell:	n/a	n/a
40	EGR1	chr22:21982323-21984614	K562	blood:	n/a	chr22:21984287-21984301
41	MYC	chr22:21982938-21984709	MCF10A-Er-Src	breast:	n/a	chr22:21983157-21983167
42	EGR1	chr22:21982456-21984627	K562	blood:	n/a	chr22:21984287-21984301
43	POLR2A	chr22:21984072-21984442	HepG2	liver:	n/a	n/a
44	TEAD4	chr22:21976201-21984706	K562	blood:	n/a	n/a
45	TBL1XR1	chr22:21982144-21984618	K562	blood:	n/a	n/a
46	IRF1	chr22:21983338-21984663	K562	blood:	n/a	n/a
47	RAD21	chr22:21984325-21984595	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr22:21984360-21984510	HFF-Myc	foreskin:	n/a	chr22:21984429-21984447 chr22:21984430-21984446
49	TCF12	chr22:21983200-21984600	ECC-1	luminal epithelium:	n/a	chr22:21984404-21984411
50	YY1	chr22:21984174-21984516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:21269803..21271886-chr22:21982813..21985485,2	K562	blood:
2	chr22:20861847..20864398-chr22:21982192..21984735,3	K562	blood:
3	chr22:20378583..20380116-chr22:21982503..21985257,2	K562	blood:
4	chr22:21982535..21985245-chr22:22018115..22021988,3	MCF-7	breast:
5	chr22:21982265..21985710-chr22:22005242..22008783,5	MCF-7	breast:
6	chr22:21983800..21985930-chr9:136215021..136217222,2	K562	blood:
7	chr22:21979187..21986650-chr22:21993296..22001177,21	MCF-7	breast:
8	chr22:21353932..21358932-chr22:21981928..21985927,5	K562	blood:
9	chr22:21821085..21824065-chr22:21983565..21985249,2	K562	blood:
10	chr22:21821074..21822903-chr22:21982952..21985553,3	K562	blood:
11	chr22:21368598..21370649-chr22:21982712..21985008,2	K562	blood:
12	chr22:21979671..21985739-chr22:22220007..22225195,6	K562	blood:
13	chr22:21921034..21925776-chr22:21981790..21988067,8	MCF-7	breast:
14	chr22:21983837..21984472-chr5:133862006..133862899,2	Hela-S3	cervix:
15	chr22:21921535..21923886-chr22:21982326..21985629,8	MCF-7	breast:
16	chr12:120728150..120730053-chr22:21983081..21985244,2	K562	blood:
17	chr19:14628735..14629532-chr22:21983809..21984400,2	Hela-S3	cervix:
18	chr22:21983948..21987333-chr22:22088191..22091412,3	K562	blood:
19	chr22:21982768..21985323-chr22:22291461..22294984,4	K562	blood:
20	chr22:21982548..21988468-chr22:22219240..22225195,10	K562	blood:
21	chr1:11968224..11970573-chr22:21982926..21985851,3	K562	blood:
22	chr22:21982497..21985083-chr22:22004368..22006741,4	MCF-7	breast:

Variant related genes	Relation type
CCDC116	TF binding region
YDJC	TF binding region
ENSG00000212102	Chromatin interaction
ENSG00000200831	Chromatin interaction
ENSG00000230513	Chromatin interaction
ENSG00000273342	Chromatin interaction
ENSG00000099942	Chromatin interaction
ENSG00000206140	Chromatin interaction
ENSG00000128228	Chromatin interaction
ENSG00000100027	Chromatin interaction
ENSG00000100034	Chromatin interaction
ENSG00000206611	Chromatin interaction
ENSG00000043143	Chromatin interaction
ENSG00000099917	Chromatin interaction
ENSG00000099957	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000100030	Chromatin interaction
ENSG00000148303	Chromatin interaction
ENSG00000207751	Chromatin interaction
ENSG00000224086	Chromatin interaction
ENSG00000184436	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000100023	Chromatin interaction
ENSG00000206176	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000185651	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1034329	0.91[ASN][1000 genomes]
rs11089629	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11089637	0.97[ASN][1000 genomes]
rs12158299	0.97[ASN][1000 genomes]
rs12169001	0.84[ASN][1000 genomes]
rs131656	0.88[ASN][1000 genomes]
rs131658	0.89[ASN][1000 genomes]
rs131664	0.91[ASN][1000 genomes]
rs131665	0.91[ASN][1000 genomes]
rs140489	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs140490	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs140491	0.91[ASN][1000 genomes]
rs140492	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs140496	0.87[ASN][1000 genomes]
rs140498	0.91[ASN][1000 genomes]
rs140499	0.91[ASN][1000 genomes]
rs1811069	0.94[ASN][1000 genomes]
rs181359	0.91[ASN][1000 genomes]
rs181360	0.91[ASN][1000 genomes]
rs181363	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs181366	0.91[ASN][1000 genomes]
rs2070512	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2266964	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2283789	0.91[ASN][1000 genomes]
rs2283790	0.97[ASN][1000 genomes]
rs2298428	0.81[EUR][1000 genomes]
rs2298429	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2876971	0.96[ASN][1000 genomes]
rs4821108	0.94[ASN][1000 genomes]
rs4821112	0.97[ASN][1000 genomes]
rs4821130	0.97[ASN][1000 genomes]
rs5749485	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5749493	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5754217	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5754238	0.85[ASN][1000 genomes]
rs5754295	0.94[ASN][1000 genomes]
rs5754323	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5754352	0.97[ASN][1000 genomes]
rs5754422	0.97[ASN][1000 genomes]
rs5754426	0.97[ASN][1000 genomes]
rs5754467	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994638	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs5998576	0.89[ASN][1000 genomes]
rs5998599	0.92[ASN][1000 genomes]
rs5998619	0.94[ASN][1000 genomes]
rs5998644	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs5998672	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs66534072	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs710177	0.98[ASN][1000 genomes]
rs73166622	0.94[ASN][1000 genomes]
rs73166632	0.91[ASN][1000 genomes]
rs738127	0.97[ASN][1000 genomes]
rs738128	0.83[ASN][1000 genomes]
rs7444	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7445	0.93[ASN][1000 genomes]
rs8137950	0.84[ASN][1000 genomes]
rs8139079	0.97[ASN][1000 genomes]
rs861857	0.95[ASN][1000 genomes]
rs878825	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9619386	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
2	nsv482690	chr22:21807513-22016791	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
3	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
4	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
5	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
6	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
7	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
8	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
9	nsv914464	chr22:21964761-22039863	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
10	nsv914465	chr22:21964761-22055280	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
11	nsv914466	chr22:21964761-22057273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
12	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
13	nsv516806	chr22:21982892-21997070	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv914467	chr22:21982892-22055280	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
15	nsv914468	chr22:21982892-22070489	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	365 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3747093	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs3747093	CCDC116	cis	lung	GTEx
rs3747093	UBE2L3	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21980600-21984800	Enhancers	Fetal Brain Male	brain
2	chr22:21982600-21984400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr22:21982800-21984600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr22:21982800-21984600	Active TSS	Fetal Brain Female	brain
5	chr22:21983000-21984400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr22:21983000-21984400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr22:21983000-21984400	Active TSS	Fetal Intestine Large	intestine
8	chr22:21983000-21984600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:21983000-21984600	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr22:21983000-21984600	Active TSS	Duodenum Mucosa	Duodenum
11	chr22:21983000-21984600	Active TSS	GM12878-XiMat	blood
12	chr22:21983000-21984600	Active TSS	Hela-S3	cervix
13	chr22:21983200-21984400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr22:21983200-21984400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr22:21983200-21984400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr22:21983200-21984400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr22:21983200-21984400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr22:21983200-21984400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr22:21983200-21984400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr22:21983200-21984400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:21983200-21984400	Active TSS	Brain Substantia Nigra	brain
22	chr22:21983200-21984400	Active TSS	Fetal Intestine Small	intestine
23	chr22:21983200-21984400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr22:21983200-21984400	Active TSS	NHLF	lung
25	chr22:21983200-21984600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr22:21983200-21984600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr22:21983200-21984600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr22:21983200-21984600	Active TSS	Brain Hippocampus Middle	brain
29	chr22:21983200-21984600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr22:21983200-21984600	Active TSS	Rectal Smooth Muscle	rectum
31	chr22:21983400-21984400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr22:21983400-21984400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:21983400-21984400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr22:21983400-21984400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:21983400-21984400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr22:21983400-21984400	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr22:21983400-21984400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:21983400-21984400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr22:21983400-21984400	Active TSS	Fetal Kidney	kidney
40	chr22:21983400-21984400	Transcr. at gene 5' and 3'	Right Atrium	heart
41	chr22:21983400-21984400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr22:21983400-21984600	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr22:21983400-21984600	Active TSS	A549	lung
44	chr22:21983400-21984600	Active TSS	HSMMtube	muscle
45	chr22:21983600-21984400	Active TSS	H1 Cell Line	embryonic stem cell
46	chr22:21983600-21984400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:21983600-21984400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:21983600-21984400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:21983600-21984400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:21983600-21984400	Active TSS	Primary T cells from cord blood	blood

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