Variant report

Variant	rs13169748
Chromosome Location	chr5:112848999-112849000
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	KAP1	chr5:112848618-112849478	K562	blood:	n/a	n/a
2	YY1	chr5:112848995-112850000	SK-N-SH	brain:	n/a	chr5:112849278-112849287
3	ZNF263	chr5:112848757-112849639	HEK293-T-REx	kidney:	n/a	chr5:112849243-112849264
4	MXI1	chr5:112848973-112850082	GM12878	blood:	n/a	n/a
5	TAF1	chr5:112848951-112849960	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr5:112848911-112849489	ECC-1	luminal epithelium:	n/a	n/a
7	RAD21	chr5:112848824-112849807	SK-N-SH	brain:	n/a	n/a
8	MAX	chr5:112848939-112849816	A549	lung:	n/a	n/a
9	TRIM28	chr5:112848944-112849198	K562	blood:	n/a	n/a
10	CBX3	chr5:112848931-112849486	K562	blood:	n/a	n/a
11	CBX3	chr5:112848883-112849810	HCT-116	colon:	n/a	n/a
12	REST	chr5:112848815-112850431	H1-neurons	neurons:	n/a	n/a
13	TRIM28	chr5:112848944-112849584	K562	blood:	n/a	n/a
14	SETDB1	chr5:112848930-112849424	U2OS	brain:	n/a	n/a
15	USF1	chr5:112848906-112849584	A549	lung:	n/a	chr5:112849331-112849347 chr5:112849332-112849348
16	ATF3	chr5:112848979-112849566	K562	blood:	n/a	chr5:112849373-112849381 chr5:112849369-112849380 chr5:112849361-112849381 chr5:112849370-112849380 chr5:112849373-112849380 chr5:112849372-112849380 chr5:112849346-112849359 chr5:112849369-112849384 chr5:112849371-112849382 chr5:112849372-112849392 chr5:112849371-112849384 chr5:112849369-112849382
17	JUN	chr5:112848816-112850505	K562	blood:	n/a	chr5:112849371-112849384 chr5:112849344-112849357 chr5:112849372-112849381
18	ATF2	chr5:112848938-112849700	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr5:112848893-112849952	HCT-116	colon:	n/a	n/a
20	CREB1	chr5:112848939-112849860	K562	blood:	n/a	chr5:112849370-112849383
21	RCOR1	chr5:112848211-112849835	IMR90	lung:	n/a	n/a
22	USF2	chr5:112848765-112849513	Hela-S3	cervix:	n/a	chr5:112849331-112849347 chr5:112849332-112849348
23	MXI1	chr5:112848600-112850607	SK-N-SH	brain:	n/a	n/a
24	MXI1	chr5:112848954-112850108	IMR90	lung:	n/a	n/a
25	USF1	chr5:112848986-112849581	SK-N-SH	brain:	n/a	chr5:112849331-112849347 chr5:112849332-112849348
26	BRCA1	chr5:112848840-112849561	Hela-S3	cervix:	n/a	n/a
27	ATF2	chr5:112848939-112849802	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:112848996-112849663	SK-N-MC	brain:	n/a	n/a
29	MAZ	chr5:112848964-112849912	K562	blood:	n/a	n/a
30	JUND	chr5:112848638-112850631	SK-N-SH	brain:	n/a	chr5:112849372-112849381
31	MAX	chr5:112848900-112850216	A549	lung:	n/a	n/a
32	PML	chr5:112848953-112850202	GM12878	blood:	n/a	n/a
33	E2F6	chr5:112848928-112849693	A549	lung:	n/a	chr5:112849371-112849380 chr5:112849280-112849292 chr5:112849531-112849540 chr5:112849281-112849292 chr5:112849373-112849382 chr5:112849278-112849287
34	CTCF	chr5:112848414-112850388	A549	lung:	n/a	chr5:112850360-112850368
35	POLR2A	chr5:112848988-112850194	H1-neurons	neurons:	n/a	n/a
36	CBX3	chr5:112848854-112849678	K562	blood:	n/a	n/a
37	HA-E2F1	chr5:112848960-112849718	MCF-7	breast:	n/a	chr5:112849371-112849380 chr5:112849280-112849292 chr5:112849531-112849540 chr5:112849373-112849382 chr5:112849278-112849287
38	TCF12	chr5:112848894-112849737	A549	lung:	n/a	n/a
39	CHD1	chr5:112848588-112850690	IMR90	lung:	n/a	n/a
40	ZNF143	chr5:112848922-112849492	K562	blood:	n/a	n/a
41	CTCF	chr5:112848994-112849890	SK-N-SH	brain:	n/a	n/a
42	SMC3	chr5:112848687-112849973	SK-N-SH	brain:	n/a	n/a
43	ARID3A	chr5:112848999-112849678	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:112848936-112850257	H1-hESC	embryonic stem cell:	n/a	n/a
45	NR2F2	chr5:112848999-112849912	K562	blood:	n/a	n/a
46	SIN3AK20	chr5:112848932-112849895	MCF-7	breast:	n/a	n/a
47	POLR2A	chr5:112848971-112849813	U87	brain:	n/a	n/a
48	MTA3	chr5:112848998-112849679	GM12878	blood:	n/a	n/a
49	RUNX3	chr5:112848934-112849712	GM12878	blood:	n/a	n/a
50	POLR2A	chr5:112848965-112849831	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:
2	chr5:112823438..112825437-chr5:112848716..112850682,3	MCF-7	breast:

Variant related genes	Relation type
YTHDC2	TF binding region
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10053341	0.86[EUR][1000 genomes]
rs10056194	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10065790	0.90[EUR][1000 genomes]
rs10071684	0.91[EUR][1000 genomes]
rs10077431	0.80[EUR][1000 genomes]
rs11241213	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13171630	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13174075	0.92[EUR][1000 genomes]
rs13182972	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13436825	0.91[EUR][1000 genomes]
rs17331844	0.90[EUR][1000 genomes]
rs17388260	0.84[EUR][1000 genomes]
rs17389165	0.96[EUR][1000 genomes]
rs1816062	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2162841	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2914198	0.83[EUR][1000 genomes]
rs2972689	0.84[EUR][1000 genomes]
rs2972690	0.84[EUR][1000 genomes]
rs33992630	0.86[EUR][1000 genomes]
rs34147627	0.84[EUR][1000 genomes]
rs34324763	0.82[EUR][1000 genomes]
rs35093510	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35193208	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35926701	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35933960	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36023163	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66540465	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66572866	0.84[EUR][1000 genomes]
rs6867579	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6871934	0.92[EUR][1000 genomes]
rs6872490	0.84[EUR][1000 genomes]
rs6879257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890874	0.93[EUR][1000 genomes]
rs71577448	0.84[EUR][1000 genomes]
rs72792189	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7706721	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7708831	0.82[EUR][1000 genomes]
rs7718203	0.90[EUR][1000 genomes]
rs8180416	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9326890	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9326891	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112847200-112849000	Enhancers	Gastric	stomach
2	chr5:112847800-112849000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112847800-112849000	Enhancers	HMEC	breast
4	chr5:112848400-112849000	Enhancers	Fetal Thymus	thymus
5	chr5:112848600-112849000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:112848600-112849000	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:112848600-112849000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:112848600-112849000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:112848600-112849000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:112848600-112849000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:112848600-112849000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr5:112848600-112849000	Enhancers	Stomach Mucosa	stomach
13	chr5:112848600-112849200	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:112848600-112849400	Flanking Active TSS	Dnd41	blood
15	chr5:112848600-112850000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr5:112848600-112850200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:112848600-112850200	Active TSS	Colon Smooth Muscle	Colon
18	chr5:112848600-112850600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:112848600-112850600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr5:112848600-112850800	Active TSS	K562	blood
21	chr5:112848800-112849000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:112848800-112849000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:112848800-112849000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:112848800-112849000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr5:112848800-112849000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
26	chr5:112848800-112849000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr5:112848800-112849000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:112848800-112849000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:112848800-112849000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr5:112848800-112849000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr5:112848800-112849000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:112848800-112849000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:112848800-112849000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:112848800-112849000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr5:112848800-112849000	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr5:112848800-112849000	Flanking Active TSS	Fetal Heart	heart
37	chr5:112848800-112849000	Enhancers	Fetal Intestine Small	intestine
38	chr5:112848800-112849000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr5:112848800-112849000	Enhancers	Fetal Muscle Leg	muscle
40	chr5:112848800-112849000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:112848800-112849000	Flanking Active TSS	HepG2	liver
42	chr5:112848800-112849000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr5:112848800-112849000	Enhancers	NH-A	brain
44	chr5:112848800-112849000	Flanking Active TSS	NHDF-Ad	bronchial
45	chr5:112848800-112849000	Flanking Active TSS	NHEK	skin
46	chr5:112848800-112849200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr5:112848800-112849200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:112848800-112849200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr5:112848800-112849200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:112848800-112849200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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