Variant report

Variant	rs13053941
Chromosome Location	chr22:31031694-31031695
allele	G/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	POLR2A	chr22:31031536-31031985	A549	lung:	n/a	n/a
2	RAD21	chr22:31030159-31033009	SK-N-SH	brain:	n/a	chr22:31030567-31030586 chr22:31031143-31031156 chr22:31030572-31030584 chr22:31032159-31032171 chr22:31031145-31031157 chr22:31031995-31032005 chr22:31031446-31031456 chr22:31031511-31031524 chr22:31030571-31030580 chr22:31031145-31031155 chr22:31030568-31030582
3	NRF1	chr22:31031127-31032043	SK-N-SH	brain:	n/a	chr22:31031731-31031740
4	TEAD4	chr22:31031323-31031975	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr22:31031528-31031954	HCT-116	colon:	n/a	n/a
6	POLR2A	chr22:31030389-31032098	HUVEC	blood vessel:	n/a	n/a
7	FOXP2	chr22:31031385-31032003	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr22:31031656-31031958	MCF10A-Er-Src	breast:	n/a	n/a
9	SRF	chr22:31031447-31031903	ECC-1	luminal epithelium:	n/a	n/a
10	RAD21	chr22:31031537-31031858	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr22:31030221-31032151	U87	brain:	n/a	n/a
12	MTA3	chr22:31031673-31032326	GM12878	blood:	n/a	n/a
13	POLR2A	chr22:31031646-31031934	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr22:31030277-31032167	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr22:31031693-31031701	GM12878	blood:	n/a	n/a
16	POLR2A	chr22:31030494-31031981	GM19193	blood:	n/a	n/a
17	POLR2A	chr22:31030291-31032145	U87	brain:	n/a	n/a
18	POLR2A	chr22:31031335-31032075	Gliobla	brain:	n/a	n/a
19	TAF1	chr22:31031339-31031954	SK-N-SH	brain:	n/a	n/a
20	MAX	chr22:31031258-31032030	A549	lung:	n/a	chr22:31031998-31032008
21	POLR2A	chr22:31031636-31031944	GM12878	blood:	n/a	n/a
22	EGR1	chr22:31031447-31031965	ECC-1	luminal epithelium:	n/a	chr22:31031611-31031625 chr22:31031730-31031740
23	MYC	chr22:31031623-31031826	MCF10A-Er-Src	breast:	n/a	n/a
24	EGR1	chr22:31031470-31031780	GM12878	blood:	n/a	chr22:31031611-31031625 chr22:31031730-31031740
25	PBX3	chr22:31030334-31031909	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr22:31031351-31031982	H1-neurons	neurons:	n/a	n/a
27	CCNT2	chr22:31031513-31032077	K562	blood:	n/a	chr22:31031558-31031567
28	POLR2A	chr22:31031671-31031915	Hela-S3	cervix:	n/a	n/a
29	RELA	chr22:31030525-31031994	GM15510	blood:	n/a	n/a
30	POLR2A	chr22:31031627-31032045	K562	blood:	n/a	n/a
31	POLR2A	chr22:31031577-31032054	GM12878	blood:	n/a	n/a
32	EGR1	chr22:31031467-31031929	ECC-1	luminal epithelium:	n/a	chr22:31031611-31031625 chr22:31031730-31031740
33	PML	chr22:31031236-31031859	GM12878	blood:	n/a	n/a
34	PAX5	chr22:31031564-31031969	GM12892	blood:	n/a	n/a
35	SMC3	chr22:31030099-31032972	SK-N-SH	brain:	n/a	chr22:31032378-31032385 chr22:31031145-31031155 chr22:31031446-31031460 chr22:31031446-31031456 chr22:31030568-31030575 chr22:31030568-31030582 chr22:31032408-31032418
36	POLR2A	chr22:31031692-31031941	Hela-S3	cervix:	n/a	n/a
37	IRF1	chr22:31031556-31031818	K562	blood:	n/a	chr22:31031584-31031598
38	TAF1	chr22:31031660-31031868	Hela-S3	cervix:	n/a	n/a
39	EP300	chr22:31030282-31032076	SK-N-SH	brain:	n/a	chr22:31031148-31031157 chr22:31031731-31031740
40	POLR2A	chr22:31030646-31031917	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr22:31031659-31031975	GM12878	blood:	n/a	n/a
42	MYC	chr22:31031598-31031876	K562	blood:	n/a	n/a
43	MAZ	chr22:31030211-31032738	IMR90	lung:	n/a	chr22:31031998-31032008 chr22:31030749-31030758
44	RUNX3	chr22:31030348-31031944	GM12878	blood:	n/a	n/a
45	POLR2A	chr22:31031330-31032026	A549	lung:	n/a	n/a
46	POLR2A	chr22:31031191-31031975	SK-N-SH	brain:	n/a	n/a
47	MAZ	chr22:31030421-31031917	GM12878	blood:	n/a	chr22:31030749-31030758
48	EGR1	chr22:31031434-31031797	GM12878	blood:	n/a	chr22:31031611-31031625 chr22:31031730-31031740
49	POLR2A	chr22:31031451-31032030	PFSK-1	brain:	n/a	n/a
50	NFIC	chr22:31031333-31032175	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:31031688-31031738	A549	lung:	n/a
2	chr22:31031670-31031720	PFSK-1	brain:	n/a
3	chr22:31031685-31031735	PFSK-1	brain:	n/a
4	chr22:31031670-31031720	A549	lung:	n/a
5	chr22:31031685-31031735	HCPEpiC	choroid plexus:	n/a
6	chr22:31031688-31031738	H1-hESC	embryonic stem cell:	embryo
7	chr22:31031670-31031720	NHBE	bronchial:	n/a
8	chr22:31031670-31031720	HEEpiC	esophagus:	n/a
9	chr22:31031670-31031720	Hepatocyte	liver:	n/a
10	chr22:31031685-31031735	GM12878	blood:	n/a
11	chr22:31031670-31031720	HNPCEpiC	eye:	n/a
12	chr22:31031688-31031738	HRE	kidney:	n/a
13	chr22:31031670-31031720	AG10803	skin:	n/a
14	chr22:31031685-31031735	HCT-116	colon:	n/a
15	chr22:31031685-31031735	NH-A	brain:	n/a
16	chr22:31031688-31031738	PFSK-1	brain:	n/a
17	chr22:31031688-31031738	GM12891	blood:	n/a
18	chr22:31031688-31031738	HRCEpiC	kidney:	n/a
19	chr22:31031688-31031738	AG09319	gingival:	n/a
20	chr22:31031688-31031738	MCF-7	breast:	n/a
21	chr22:31031688-31031738	PrEC	prostate:	n/a
22	chr22:31031688-31031738	GM19239	blood:	n/a
23	chr22:31031688-31031738	GM06990	blood:	n/a
24	chr22:31031685-31031735	NHBE	bronchial:	n/a
25	chr22:31031685-31031735	HRPEpiC	eye:	n/a
26	chr22:31031670-31031720	HRPEpiC	eye:	n/a
27	chr22:31031688-31031738	CMK	blood:	n/a
28	chr22:31031685-31031735	CMK	blood:	n/a
29	chr22:31031685-31031735	A549	lung:	n/a
30	chr22:31031670-31031720	AG04450	lung:	fetal
31	chr22:31031685-31031735	ECC-1	luminal epithelium:	n/a
32	chr22:31031688-31031738	HCPEpiC	choroid plexus:	n/a
33	chr22:31031670-31031720	Caco-2	colon:	n/a
34	chr22:31031670-31031720	HRCEpiC	kidney:	n/a
35	chr22:31031670-31031720	LNCaP	prostate:	n/a
36	chr22:31031670-31031720	AG04449	skin:	fetal
37	chr22:31031670-31031720	HUVEC	blood vessel:	n/a
38	chr22:31031688-31031738	K562	blood:	n/a
39	chr22:31031670-31031720	BE2_C	brain:	n/a
40	chr22:31031670-31031720	GM12892	blood:	n/a
41	chr22:31031670-31031720	HEK293	kidney:	embryo
42	chr22:31031688-31031738	HMEC	breast:	n/a
43	chr22:31031670-31031720	HL-60	blood:	n/a
44	chr22:31031685-31031735	PANC-1	pancreas:	n/a
45	chr22:31031688-31031738	GM12878	blood:	n/a
46	chr22:31031688-31031738	NHDF-neo	bronchial:	n/a
47	chr22:31031670-31031720	ECC-1	luminal epithelium:	n/a
48	chr22:31031670-31031720	HAEpiC	amniotic membrane:	n/a
49	chr22:31031670-31031720	HCT-116	colon:	n/a
50	chr22:31031685-31031735	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31030552..31033273-chr22:31061698..31065017,4	MCF-7	breast:
2	chr22:31031588..31032094-chr22:31090123..31090949,2	MCF-7	breast:
3	chr22:31030338..31033016-chr22:31062140..31065480,4	MCF-7	breast:

Variant related genes	Relation type
SLC35E4	TF binding region
SLC35E4	CpG island
ENSG00000184792	Chromatin interaction
ENSG00000167065	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13054505	0.91[EUR][1000 genomes]
rs1544468	0.89[EUR][1000 genomes]
rs2003503	0.86[ASN][1000 genomes]
rs2078973	0.81[ASN][1000 genomes]
rs3179442	0.82[EUR][1000 genomes]
rs4340628	0.86[ASN][1000 genomes]
rs4353747	0.90[EUR][1000 genomes]
rs5749142	0.90[EUR][1000 genomes]
rs5749143	0.90[EUR][1000 genomes]
rs5749145	0.90[EUR][1000 genomes]
rs5749148	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753257	0.90[EUR][1000 genomes]
rs5753258	0.85[EUR][1000 genomes]
rs5753260	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997709	0.87[EUR][1000 genomes]
rs5997710	0.90[EUR][1000 genomes]
rs7289553	0.90[EUR][1000 genomes]
rs731990	0.89[EUR][1000 genomes]
rs731991	0.90[EUR][1000 genomes]
rs8138932	0.84[EUR][1000 genomes];0.88[ASN][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	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
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv829172	chr22:31024057-31032291	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3374115	chr22:31030477-31033325	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13053941	SLC35E4	cis	brain	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31030400-31031800	Enhancers	Liver	Liver
2	chr22:31030600-31031800	Enhancers	Primary hematopoietic stem cells	blood
3	chr22:31030600-31031800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr22:31030600-31032000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr22:31030600-31032000	Enhancers	Fetal Brain Male	brain
6	chr22:31030600-31032200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr22:31030600-31032400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr22:31030600-31032800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:31030600-31032800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr22:31030600-31032800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:31030600-31033000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr22:31030600-31033200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr22:31030600-31033200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr22:31030600-31033400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr22:31030600-31033400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr22:31030600-31033400	Flanking Active TSS	Colonic Mucosa	Colon
17	chr22:31030600-31033400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr22:31030600-31034000	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr22:31030600-31034200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr22:31030600-31034200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr22:31030600-31034400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr22:31030800-31032200	Active TSS	Fetal Kidney	kidney
23	chr22:31030800-31032400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr22:31030800-31032400	Active TSS	Brain Angular Gyrus	brain
25	chr22:31030800-31032400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr22:31030800-31032600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr22:31030800-31032600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr22:31030800-31032600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr22:31030800-31032800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr22:31030800-31033200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr22:31030800-31033400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr22:31030800-31033400	Active TSS	Psoas Muscle	Psoas
33	chr22:31030800-31033600	Active TSS	Brain Anterior Caudate	brain
34	chr22:31031000-31032000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr22:31031000-31032000	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr22:31031000-31032000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr22:31031000-31032000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:31031000-31032000	Enhancers	Fetal Heart	heart
39	chr22:31031000-31032000	Active TSS	Gastric	stomach
40	chr22:31031000-31032000	Active TSS	Right Ventricle	heart
41	chr22:31031000-31032200	Active TSS	Ovary	ovary
42	chr22:31031000-31032800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:31031000-31033400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:31031000-31033600	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr22:31031200-31032000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr22:31031200-31032000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr22:31031200-31032000	Active TSS	Esophagus	oesophagus
48	chr22:31031200-31032200	Active TSS	Left Ventricle	heart
49	chr22:31031200-31032200	Active TSS	Small Intestine	intestine
50	chr22:31031200-31032400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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