Variant report

Variant	rs5753117
Chromosome Location	chr22:30783551-30783552
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	chr22:30783203-30783834	K562	blood:	n/a	chr22:30783491-30783504 chr22:30783820-30783833 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
2	CTCF	chr22:30783395-30783637	ECC-1	luminal epithelium:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
3	CTCF	chr22:30783460-30783610	HRE	kidney:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
4	RCOR1	chr22:30783453-30783675	GM12878	blood:	n/a	n/a
5	HCFC1	chr22:30783365-30783655	K562	blood:	n/a	n/a
6	SIN3A	chr22:30782727-30783777	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr22:30783192-30783776	H1-hESC	embryonic stem cell:	n/a	chr22:30783487-30783506 chr22:30783491-30783505 chr22:30783519-30783532 chr22:30783491-30783501 chr22:30783651-30783660 chr22:30783490-30783503
8	CHD2	chr22:30783518-30783620	HepG2	liver:	n/a	n/a
9	CTCF	chr22:30783440-30783590	HUVEC	blood vessel:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
10	CTCF	chr22:30783460-30783610	HA-sp	spinal cord:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
11	CTCF	chr22:30783401-30783654	A549	lung:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
12	RAD21	chr22:30783235-30783704	SK-N-SH_RA	brain:	n/a	chr22:30783487-30783506 chr22:30783491-30783505 chr22:30783519-30783532 chr22:30783491-30783501 chr22:30783651-30783660 chr22:30783490-30783503
13	CTCF	chr22:30783440-30783590	WERI-Rb-1	eye:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
14	CTCF	chr22:30783420-30783570	GM12878	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
15	CTCF	chr22:30783420-30783570	GM12865	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
16	BACH1	chr22:30783479-30783663	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAZ	chr22:30782923-30783659	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr22:30783480-30783630	HBMEC	blood vessel:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
19	CTCF	chr22:30783440-30783590	HEK293	kidney:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
20	RAD21	chr22:30783319-30783687	A549	lung:	n/a	chr22:30783487-30783506 chr22:30783491-30783505 chr22:30783519-30783532 chr22:30783491-30783501 chr22:30783651-30783660 chr22:30783490-30783503
21	POLR2A	chr22:30783463-30783745	PFSK-1	brain:	n/a	n/a
22	CTCF	chr22:30783381-30783667	GM13977	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
23	JUND	chr22:30783435-30783665	K562	blood:	n/a	n/a
24	TEAD4	chr22:30783399-30783774	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr22:30783303-30783678	SK-N-SH_RA	brain:	n/a	chr22:30783487-30783506 chr22:30783491-30783505 chr22:30783519-30783532 chr22:30783491-30783501 chr22:30783651-30783660 chr22:30783490-30783503
26	CCNT2	chr22:30782981-30783651	K562	blood:	n/a	n/a
27	CHD2	chr22:30783024-30783733	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr22:30783440-30783590	GM12867	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
29	RCOR1	chr22:30783439-30783653	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr22:30783363-30783729	MCF-7	breast:	n/a	chr22:30783487-30783506 chr22:30783491-30783505 chr22:30783519-30783532 chr22:30783491-30783501 chr22:30783651-30783660 chr22:30783490-30783503
31	CTCF	chr22:30783480-30783630	GM06990	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
32	CTCF	chr22:30783460-30783610	HBMEC	blood vessel:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
33	CTCF	chr22:30783460-30783610	GM12866	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
34	CTCF	chr22:30783520-30783670	GM12870	blood:	n/a	n/a
35	CTCF	chr22:30783420-30783570	HepG2	liver:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
36	CTCF	chr22:30783440-30783590	HepG2	liver:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
37	ZBTB7A	chr22:30783233-30783693	HepG2	liver:	n/a	chr22:30783490-30783499
38	CTCF	chr22:30783440-30783590	SK-N-SH_RA	brain:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
39	CTCF	chr22:30783460-30783610	HMF	breast:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
40	CTCF	chr22:30783420-30783570	HRE	kidney:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
41	POLR2A	chr22:30782819-30783725	ECC-1	luminal epithelium:	n/a	n/a
42	MXI1	chr22:30783460-30783678	H1-hESC	embryonic stem cell:	n/a	n/a
43	STAT1	chr22:30783351-30783616	GM12878	blood:	n/a	n/a
44	CTCF	chr22:30783387-30783824	GM10248	blood:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
45	SMC3	chr22:30782783-30784052	SK-N-SH	brain:	n/a	chr22:30783491-30783501 chr22:30783823-30783833 chr22:30783491-30783505 chr22:30783819-30783833 chr22:30783715-30783722 chr22:30783498-30783505
46	POLR2A	chr22:30783419-30783704	U87	brain:	n/a	n/a
47	CREB1	chr22:30782930-30783780	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr22:30783440-30783590	NHEK	skin:	n/a	chr22:30783491-30783504 chr22:30783489-30783507 chr22:30783490-30783506 chr22:30783484-30783505 chr22:30783495-30783504 chr22:30783491-30783504 chr22:30783492-30783502
49	POLR2A	chr22:30782918-30783733	H1-hESC	embryonic stem cell:	n/a	n/a
50	EP300	chr22:30783541-30783632	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30658407..30662211-chr22:30782039..30784785,6	MCF-7	breast:
2	chr22:30659097..30662032-chr22:30782521..30784593,3	MCF-7	breast:
3	chr22:30751699..30753468-chr22:30782814..30784590,2	K562	blood:
4	chr22:30681125..30685749-chr22:30780011..30785695,7	MCF-7	breast:
5	chr22:30683553..30684657-chr22:30783449..30783965,3	K562	blood:
6	chr22:30781850..30784098-chr22:30791520..30793035,3	MCF-7	breast:
7	chr22:30721494..30724747-chr22:30781448..30784941,5	MCF-7	breast:
8	chr22:30683315..30684641-chr22:30783196..30784353,5	MCF-7	breast:
9	chr22:30783511..30785819-chr22:30839208..30841180,2	K562	blood:
10	chr22:30683076..30686857-chr22:30780059..30784684,12	MCF-7	breast:
11	chr22:30684150..30686115-chr22:30783000..30785215,3	K562	blood:
12	chr22:30783066..30785199-chr22:30819529..30822458,2	K562	blood:
13	chr22:30768241..30771846-chr22:30779941..30783662,3	MCF-7	breast:
14	chr22:30683337..30684429-chr22:30783040..30783917,8	MCF-7	breast:

Variant related genes	Relation type
RNF215	TF binding region
ENSG00000099992	Chromatin interaction
ENSG00000187860	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000099985	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000100003	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1061660	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1061664	0.89[MEX][hapmap]
rs12106618	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476659	0.86[GIH][hapmap]
rs2018514	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072157	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072158	0.87[ASW][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap]
rs2072159	0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap]
rs2074651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2074732	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap]
rs2240422	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs2283868	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283869	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28523826	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820003	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap]
rs4820010	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749090	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753092	0.81[EUR][1000 genomes]
rs5753093	0.81[EUR][1000 genomes]
rs5753109	0.81[EUR][1000 genomes]
rs5753116	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997628	0.81[EUR][1000 genomes]
rs5997629	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997641	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7292744	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73390209	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757660	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757870	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs8138401	0.82[EUR][1000 genomes]
rs887098	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	esv3376959	chr22:30782102-30785000	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	esv3374389	chr22:30782177-30784725	Flanking Active TSS Active TSS Enhancers Weak transcription 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5753117	C22orf31	cis	cerebellum	SCAN
rs5753117	LIF	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30782200-30783600	Enhancers	Fetal Heart	heart
2	chr22:30782200-30783800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr22:30782200-30784000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr22:30782400-30783600	Active TSS	Psoas Muscle	Psoas
5	chr22:30782400-30783800	Enhancers	Primary T cells from cord blood	blood
6	chr22:30782400-30783800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr22:30782600-30783800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr22:30782600-30783800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr22:30782600-30783800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:30782600-30783800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr22:30782600-30783800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:30782600-30783800	Active TSS	Fetal Kidney	kidney
13	chr22:30782800-30783600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:30782800-30783600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:30782800-30783600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:30782800-30783600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr22:30782800-30783600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:30782800-30783600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr22:30782800-30783600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:30782800-30783600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr22:30782800-30783600	Active TSS	Muscle Satellite Cultured Cells	--
22	chr22:30782800-30783600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:30782800-30783600	Active TSS	Aorta	Aorta
24	chr22:30782800-30783600	Active TSS	Brain Angular Gyrus	brain
25	chr22:30782800-30783600	Active TSS	Brain Anterior Caudate	brain
26	chr22:30782800-30783600	Active TSS	Brain Cingulate Gyrus	brain
27	chr22:30782800-30783600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr22:30782800-30783600	Active TSS	Colonic Mucosa	Colon
29	chr22:30782800-30783600	Active TSS	Esophagus	oesophagus
30	chr22:30782800-30783600	Active TSS	Fetal Brain Female	brain
31	chr22:30782800-30783600	Active TSS	Fetal Lung	lung
32	chr22:30782800-30783600	Active TSS	Fetal Stomach	stomach
33	chr22:30782800-30783600	Active TSS	Pancreas	Pancrea
34	chr22:30782800-30783600	Active TSS	Rectal Smooth Muscle	rectum
35	chr22:30782800-30783600	Active TSS	Right Atrium	heart
36	chr22:30782800-30783600	Bivalent/Poised TSS	Thymus	Thymus
37	chr22:30782800-30783600	Active TSS	HepG2	liver
38	chr22:30782800-30783600	Active TSS	HSMMtube	muscle
39	chr22:30782800-30783600	Active TSS	HUVEC	blood vessel
40	chr22:30782800-30783600	Active TSS	NHDF-Ad	bronchial
41	chr22:30782800-30783600	Active TSS	NHEK	skin
42	chr22:30782800-30783600	Active TSS	NHLF	lung
43	chr22:30782800-30783800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr22:30782800-30783800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr22:30782800-30783800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr22:30782800-30783800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:30782800-30783800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr22:30782800-30783800	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr22:30782800-30783800	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr22:30782800-30783800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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