Variant report

Variant	rs5753446
Chromosome Location	chr22:31451964-31451965
allele	C/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	EP300	chr22:31451318-31452106	T-47D	breast:	n/a	chr22:31451800-31451816 chr22:31451732-31451742
2	RAD21	chr22:31451596-31451989	HepG2	liver:	n/a	n/a
3	MAZ	chr22:31450943-31452206	IMR90	lung:	n/a	chr22:31451761-31451770
4	HDAC2	chr22:31451455-31452068	MCF-7	breast:	n/a	n/a
5	MBD4	chr22:31451473-31452038	HepG2	liver:	n/a	n/a
6	MAX	chr22:31451386-31452095	ECC-1	luminal epithelium:	n/a	chr22:31451761-31451770
7	PBX3	chr22:31451496-31451988	SK-N-SH	brain:	n/a	n/a
8	MAX	chr22:31451118-31452248	A549	lung:	n/a	chr22:31451761-31451770
9	EP300	chr22:31451353-31452100	ECC-1	luminal epithelium:	n/a	chr22:31451800-31451816 chr22:31451732-31451742
10	EP300	chr22:31451325-31452129	A549	lung:	n/a	chr22:31451800-31451816 chr22:31451732-31451742
11	REST	chr22:31451464-31452008	A549	lung:	n/a	n/a
12	CEBPB	chr22:31451500-31451973	Hela-S3	cervix:	n/a	chr22:31451761-31451772
13	EP300	chr22:31451474-31452017	HepG2	liver:	n/a	chr22:31451800-31451816 chr22:31451732-31451742
14	USF1	chr22:31451521-31452024	A549	lung:	n/a	n/a
15	CREB1	chr22:31451397-31452093	HepG2	liver:	n/a	chr22:31451682-31451695
16	MXI1	chr22:31451293-31452193	IMR90	lung:	n/a	n/a
17	MAX	chr22:31451045-31452362	A549	lung:	n/a	chr22:31451761-31451770
18	E2F6	chr22:31451407-31451983	H1-hESC	embryonic stem cell:	n/a	chr22:31451648-31451655 chr22:31451644-31451656 chr22:31451645-31451660 chr22:31451648-31451655 chr22:31451685-31451694 chr22:31451648-31451655
19	CEBPB	chr22:31451343-31452150	A549	lung:	n/a	chr22:31451761-31451772
20	FOSL2	chr22:31451515-31452029	HepG2	liver:	n/a	chr22:31451684-31451693
21	ATF3	chr22:31451435-31451986	A549	lung:	n/a	n/a
22	RFX5	chr22:31451544-31451999	Hela-S3	cervix:	n/a	n/a
23	KAP1	chr22:31451370-31452073	HEK293	kidney:	n/a	n/a
24	TCF12	chr22:31451457-31451966	A549	lung:	n/a	n/a
25	CHD2	chr22:31451589-31452058	HepG2	liver:	n/a	n/a
26	JUND	chr22:31451342-31452048	T-47D	breast:	n/a	chr22:31451684-31451693
27	MAZ	chr22:31451601-31452051	HepG2	liver:	n/a	chr22:31451761-31451770
28	NFIC	chr22:31451486-31452031	HepG2	liver:	n/a	chr22:31451597-31451625
29	CREB1	chr22:31451486-31452011	A549	lung:	n/a	chr22:31451682-31451695
30	RCOR1	chr22:31450865-31452901	IMR90	lung:	n/a	n/a
31	BHLHE40	chr22:31451552-31452058	HepG2	liver:	n/a	n/a
32	CEBPB	chr22:31451539-31451970	ECC-1	luminal epithelium:	n/a	chr22:31451761-31451772
33	CEBPB	chr22:31451503-31451967	IMR90	lung:	n/a	chr22:31451761-31451772
34	CEBPD	chr22:31451549-31452004	HepG2	liver:	n/a	n/a
35	STAT3	chr22:31451533-31451970	MCF10A-Er-Src	breast:	n/a	n/a
36	MAX	chr22:31451369-31452058	HCT-116	colon:	n/a	chr22:31451761-31451770
37	ATF3	chr22:31451493-31452037	A549	lung:	n/a	n/a
38	TEAD4	chr22:31451513-31452048	ECC-1	luminal epithelium:	n/a	n/a
39	MAFK	chr22:31451598-31452090	HepG2	liver:	n/a	n/a
40	HDAC2	chr22:31451575-31452019	MCF-7	breast:	n/a	n/a
41	EP300	chr22:31451570-31452056	HepG2	liver:	n/a	chr22:31451800-31451816 chr22:31451732-31451742
42	BCL3	chr22:31451404-31452226	A549	lung:	n/a	n/a
43	STAT1	chr22:31451385-31451989	Hela-S3	cervix:	n/a	n/a
44	FOSL2	chr22:31451350-31452159	A549	lung:	n/a	chr22:31451684-31451693
45	MAFF	chr22:31451555-31452151	HepG2	liver:	n/a	n/a
46	SETDB1	chr22:31451332-31451965	U2OS	brain:	n/a	n/a
47	MYBL2	chr22:31451436-31452087	HepG2	liver:	n/a	n/a
48	YY1	chr22:31451487-31451982	HepG2	liver:	n/a	n/a
49	FOSL2	chr22:31451488-31452021	HepG2	liver:	n/a	chr22:31451684-31451693
50	CREB1	chr22:31451453-31451986	ECC-1	luminal epithelium:	n/a	chr22:31451682-31451695

No.	Distal block	Cell Line	Cell type
1	chr22:31445856..31448467-chr22:31451849..31454142,3	K562	blood:
2	chr22:31450684..31454190-chr22:31458624..31461519,3	K562	blood:
3	chr22:31449984..31454484-chr22:31456787..31462654,7	K562	blood:
4	chr22:31360377..31363179-chr22:31451258..31453241,3	K562	blood:
5	chr22:31451720..31453462-chr22:31457824..31459739,2	MCF-7	breast:
6	chr22:31363469..31366268-chr22:31450278..31456884,6	MCF-7	breast:
7	chr22:31448944..31454267-chr22:31475725..31482456,15	MCF-7	breast:
8	chr22:31450722..31454659-chr22:31476861..31481048,4	K562	blood:
9	chr22:31362787..31366384-chr22:31450123..31453347,3	MCF-7	breast:
10	chr22:31450718..31452880-chr22:31457371..31459942,3	MCF-7	breast:
11	chr22:31450083..31452668-chr22:31463620..31466392,3	MCF-7	breast:
12	chr22:31449294..31454779-chr22:31475265..31480255,11	MCF-7	breast:
13	chr22:31432776..31435079-chr22:31450665..31453170,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL633P	TF binding region
ENSG00000273387	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000133422	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11705137	1.00[CHD][hapmap]
rs12167220	1.00[CHD][hapmap]
rs12485186	1.00[ASN][1000 genomes]
rs1990125	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017301	1.00[CHD][hapmap]
rs2413016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820933	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56017492	1.00[ASN][1000 genomes]
rs5753431	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs5753449	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5997854	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73156781	1.00[ASN][1000 genomes]
rs73156787	1.00[ASN][1000 genomes]
rs73156792	1.00[ASN][1000 genomes]
rs73156799	0.87[ASN][1000 genomes]
rs917208	1.00[CHD][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs9621188	1.00[CHD][hapmap]

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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv966103	chr22:31410201-31452981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5753446	C22orf42	cis	cerebellum	SCAN
rs5753446	SLC35E4	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31440000-31453200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr22:31441600-31455000	Enhancers	Fetal Stomach	stomach
3	chr22:31443600-31455400	Weak transcription	K562	blood
4	chr22:31449200-31453400	Enhancers	Fetal Muscle Leg	muscle
5	chr22:31449800-31453200	Enhancers	Fetal Lung	lung
6	chr22:31450000-31453000	Enhancers	Fetal Muscle Trunk	muscle
7	chr22:31450200-31452400	Enhancers	Fetal Heart	heart
8	chr22:31450200-31454400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr22:31450600-31452200	Enhancers	NHLF	lung
10	chr22:31450800-31452000	Enhancers	Lung	lung
11	chr22:31450800-31452800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr22:31450800-31452800	Enhancers	Left Ventricle	heart
13	chr22:31450800-31453000	Enhancers	Placenta	Placenta
14	chr22:31450800-31453200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr22:31450800-31453200	Enhancers	Fetal Intestine Small	intestine
16	chr22:31450800-31453600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:31450800-31454600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:31451000-31452000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr22:31451000-31452000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:31451000-31452000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr22:31451000-31452000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr22:31451000-31452000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:31451000-31452000	Enhancers	Adipose Nuclei	Adipose
24	chr22:31451000-31452000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr22:31451000-31452000	Enhancers	Pancreas	Pancrea
26	chr22:31451000-31452000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr22:31451000-31452000	Enhancers	HUVEC	blood vessel
28	chr22:31451000-31452200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr22:31451000-31452200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr22:31451000-31452200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:31451000-31452200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr22:31451000-31452200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr22:31451000-31452200	Enhancers	Brain Germinal Matrix	brain
34	chr22:31451000-31452200	Enhancers	Ovary	ovary
35	chr22:31451000-31452200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr22:31451000-31452200	Enhancers	HSMM	muscle
37	chr22:31451000-31452200	Enhancers	NHDF-Ad	bronchial
38	chr22:31451000-31452200	Enhancers	NHEK	skin
39	chr22:31451000-31452200	Enhancers	Osteobl	bone
40	chr22:31451000-31452400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr22:31451000-31452800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr22:31451000-31452800	Enhancers	HMEC	breast
43	chr22:31451000-31453200	Enhancers	Fetal Intestine Large	intestine
44	chr22:31451000-31453400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr22:31451000-31453400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:31451200-31452000	Enhancers	Brain Angular Gyrus	brain
47	chr22:31451200-31452000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr22:31451200-31452000	Flanking Active TSS	Hela-S3	cervix
49	chr22:31451200-31452000	Enhancers	NH-A	brain
50	chr22:31451200-31452200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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