Variant report

Variant	rs2242482
Chromosome Location	chr13:50655879-50655880
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	TEAD4	chr13:50655620-50655958	K562	blood:	n/a	n/a
2	HEY1	chr13:50655720-50656232	K562	blood:	n/a	n/a
3	MYBL2	chr13:50655800-50657358	HepG2	liver:	n/a	n/a
4	POLR2A	chr13:50655526-50656507	A549	lung:	n/a	n/a
5	POLR2A	chr13:50654399-50657316	HepG2	liver:	n/a	n/a
6	CTCF	chr13:50655800-50655950	AG10803	skin:	n/a	n/a
7	YY1	chr13:50655077-50656398	SK-N-SH	brain:	n/a	chr13:50656171-50656182 chr13:50655740-50655751 chr13:50656171-50656180 chr13:50655785-50655799 chr13:50655787-50655796 chr13:50655790-50655799
8	CTCF	chr13:50655800-50655950	GM12866	blood:	n/a	n/a
9	CBX3	chr13:50655531-50657127	K562	blood:	n/a	n/a
10	POU2F2	chr13:50655691-50657015	GM12878	blood:	n/a	chr13:50655748-50655760 chr13:50656285-50656297
11	POLR2A	chr13:50655821-50657059	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr13:50655855-50656102	IMR90	lung:	n/a	n/a
13	CTCF	chr13:50655780-50655930	A549	lung:	n/a	n/a
14	CHD2	chr13:50655284-50656829	K562	blood:	n/a	chr13:50656294-50656304 chr13:50655742-50655752
15	YY1	chr13:50655079-50656504	GM12891	blood:	n/a	chr13:50656171-50656182 chr13:50655740-50655751 chr13:50656171-50656180 chr13:50655785-50655799 chr13:50655787-50655796 chr13:50655790-50655799
16	CTCF	chr13:50655840-50655990	GM12878	blood:	n/a	n/a
17	RUNX3	chr13:50655488-50657036	GM12878	blood:	n/a	n/a
18	CTCF	chr13:50655740-50655890	RPTEC	kidney:	n/a	n/a
19	CTCF	chr13:50655740-50655890	HCM	heart:	n/a	n/a
20	E2F4	chr13:50655561-50656388	Hela-S3	cervix:	n/a	chr13:50655692-50655702 chr13:50655788-50655798 chr13:50655787-50655796 chr13:50656266-50656275 chr13:50656187-50656202 chr13:50656171-50656180
21	STAT1	chr13:50655652-50656944	GM12878	blood:	n/a	n/a
22	CTCF	chr13:50655840-50655990	SK-N-SH_RA	brain:	n/a	n/a
23	TAF1	chr13:50655016-50657089	ECC-1	luminal epithelium:	n/a	n/a
24	CTCF	chr13:50655797-50656081	GM12892	blood:	n/a	n/a
25	YY1	chr13:50655843-50656346	K562	blood:	n/a	chr13:50656171-50656182 chr13:50656171-50656180
26	YY1	chr13:50655847-50656372	SK-N-SH_RA	brain:	n/a	chr13:50656171-50656182 chr13:50656171-50656180
27	CTCF	chr13:50655840-50655990	BE2_C	brain:	n/a	n/a
28	SMARCB1	chr13:50655139-50656456	Hela-S3	cervix:	n/a	n/a
29	YY1	chr13:50655842-50656280	GM12892	blood:	n/a	chr13:50656171-50656182 chr13:50656171-50656180
30	BHLHE40	chr13:50654913-50657076	GM12878	blood:	n/a	chr13:50655688-50655704 chr13:50655704-50655720
31	CTCF	chr13:50655840-50655990	SAEC	small airway:	n/a	n/a
32	POLR2A	chr13:50655083-50657045	K562	blood:	n/a	n/a
33	EP300	chr13:50655550-50657177	K562	blood:	n/a	chr13:50656995-50657009 chr13:50655870-50655886 chr13:50655873-50655886
34	SIN3AK20	chr13:50655171-50657097	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr13:50655878-50655880	MCF-7	breast:	n/a	n/a
36	MAZ	chr13:50655566-50657451	IMR90	lung:	n/a	chr13:50656289-50656299 chr13:50656286-50656296
37	CTCF	chr13:50655760-50655910	HA-sp	spinal cord:	n/a	n/a
38	MYC	chr13:50655359-50657278	K562	blood:	n/a	chr13:50656304-50656314 chr13:50656289-50656299 chr13:50656286-50656296
39	POLR2A	chr13:50653973-50657240	K562	blood:	n/a	n/a
40	POLR2A	chr13:50655696-50656262	GM12891	blood:	n/a	n/a
41	POLR2A	chr13:50655822-50656628	HepG2	liver:	n/a	n/a
42	CTCF	chr13:50655820-50655970	HRE	kidney:	n/a	n/a
43	GATA1	chr13:50655794-50657455	PBDE	blood:	n/a	n/a
44	HEY1	chr13:50655778-50656582	HepG2	liver:	n/a	n/a
45	BCLAF1	chr13:50655752-50656415	GM12878	blood:	n/a	chr13:50655787-50655800 chr13:50656173-50656182 chr13:50655789-50655798 chr13:50655786-50655799
46	UBTF	chr13:50654220-50657071	K562	blood:	n/a	n/a
47	SIN3A	chr13:50654530-50657306	H1-hESC	embryonic stem cell:	n/a	chr13:50655747-50655760
48	TCF12	chr13:50654945-50656924	A549	lung:	n/a	n/a
49	POLR2A	chr13:50655139-50656482	GM12878	blood:	n/a	n/a
50	MYC	chr13:50655667-50657023	K562	blood:	n/a	chr13:50656304-50656314 chr13:50656289-50656299 chr13:50656286-50656296

No.	Distal block	Cell Line	Cell type
1	chr13:50655118..50657080-chr13:51484545..51486295,2	K562	blood:
2	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
3	chr13:50365172..50367900-chr13:50655465..50657230,2	K562	blood:
4	chr13:50570939..50571889-chr13:50655239..50655940,2	Hela-S3	cervix:
5	chr13:50569852..50573038-chr13:50651628..50659276,11	K562	blood:
6	chr13:50569748..50573186-chr13:50654848..50657793,4	MCF-7	breast:
7	chr13:50655578..50656419-chr13:111367193..111368117,2	Hela-S3	cervix:
8	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:
9	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:
10	chr13:50655775..50656425-chr2:73143170..73143690,2	HCT-116	colon:
11	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
12	chr13:50645718..50648310-chr13:50652570..50656008,3	MCF-7	breast:
13	chr13:50654380..50657403-chr13:51482897..51486295,4	K562	blood:
14	chr13:50570665..50571474-chr13:50655702..50656445,2	NB4	blood:
15	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:

Variant related genes	Relation type
DLEU1	TF binding region
ENSG00000264864	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000135638	Chromatin interaction
ENSG00000102753	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1326120	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2066558	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2066571	0.80[ASN][1000 genomes]
rs2066572	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2066587	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2066591	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066594	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2687950	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2740508	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2740544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2760914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2803839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2812204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812216	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812217	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2997624	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4942899	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4942901	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7338055	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs7986337	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs9535407	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap]
rs9568354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap]
rs9568357	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs9568363	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568364	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs9596215	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9596219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9596220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2242482	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs2242482	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2242482	PHF11	cis	cerebellum	SCAN
rs2242482	KCNRG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50648400-50657400	Active TSS	GM12878-XiMat	blood
2	chr13:50651600-50656800	Active TSS	Fetal Thymus	thymus
3	chr13:50651600-50657200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:50651800-50656600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:50651800-50658200	Active TSS	HMEC	breast
6	chr13:50651800-50659600	Active TSS	K562	blood
7	chr13:50652200-50656600	Active TSS	Fetal Brain Female	brain
8	chr13:50652200-50658000	Active TSS	HSMMtube	muscle
9	chr13:50652400-50656600	Active TSS	Fetal Muscle Leg	muscle
10	chr13:50652400-50656800	Active TSS	Brain Anterior Caudate	brain
11	chr13:50652400-50657200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:50652400-50657200	Active TSS	Aorta	Aorta
13	chr13:50652400-50657400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:50652400-50657400	Active TSS	Psoas Muscle	Psoas
15	chr13:50652400-50657600	Active TSS	Thymus	Thymus
16	chr13:50652400-50658000	Active TSS	Hela-S3	cervix
17	chr13:50652600-50656600	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr13:50652600-50657200	Active TSS	Muscle Satellite Cultured Cells	--
19	chr13:50652600-50657400	Active TSS	HSMM	muscle
20	chr13:50652600-50657800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:50652600-50657800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr13:50652800-50656600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr13:50652800-50657800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:50652800-50657800	Active TSS	NHDF-Ad	bronchial
25	chr13:50652800-50658200	Active TSS	A549	lung
26	chr13:50653000-50656600	Active TSS	Brain Hippocampus Middle	brain
27	chr13:50653000-50657400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:50653000-50657800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:50653000-50658200	Active TSS	Fetal Intestine Large	intestine
30	chr13:50653000-50658200	Active TSS	NH-A	brain
31	chr13:50653200-50656200	Active TSS	Duodenum Mucosa	Duodenum
32	chr13:50653200-50656400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr13:50653200-50656400	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr13:50653200-50657200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:50653200-50657200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr13:50653200-50657800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:50653200-50657800	Active TSS	Fetal Heart	heart
38	chr13:50653200-50658000	Active TSS	NHLF	lung
39	chr13:50653400-50656600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:50653400-50656600	Active TSS	Primary B cells from peripheral blood	blood
41	chr13:50653400-50657000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:50653400-50657000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr13:50653400-50657000	Active TSS	Osteobl	bone
44	chr13:50653400-50657400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:50653400-50657400	Active TSS	Right Atrium	heart
46	chr13:50653400-50658000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:50653600-50656600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr13:50653600-50656600	Active TSS	HUVEC	blood vessel
49	chr13:50653600-50656800	Active TSS	Brain Substantia Nigra	brain
50	chr13:50653600-50657000	Active TSS	Fetal Kidney	kidney

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