Variant report

Variant	rs11557629
Chromosome Location	chr3:48732223-48732224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48731942-48732229	HUVEC	blood vessel:	n/a	n/a
2	YY1	chr3:48731949-48732563	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr3:48731875-48732565	SK-N-SH	brain:	n/a	n/a
4	FOS	chr3:48731752-48732465	HUVEC	blood vessel:	n/a	n/a
5	RFX5	chr3:48732121-48732478	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:48732152-48733157	GM12892	blood:	n/a	n/a
7	EP300	chr3:48732001-48732503	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr3:48732111-48733278	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF2	chr3:48732162-48732505	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:48732175-48732459	K562	blood:	n/a	n/a
11	MAX	chr3:48732028-48732586	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr3:48731804-48732759	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr3:48732032-48732523	MCF10A-Er-Src	breast:	n/a	n/a
14	YY1	chr3:48732183-48732593	SK-N-SH_RA	brain:	n/a	n/a
15	CEBPB	chr3:48732054-48732591	A549	lung:	n/a	chr3:48732320-48732331
16	NFIC	chr3:48731962-48732734	ECC-1	luminal epithelium:	n/a	n/a
17	CEBPB	chr3:48731953-48732542	Hela-S3	cervix:	n/a	chr3:48732320-48732331
18	POLR2A	chr3:48732215-48733242	GM12891	blood:	n/a	n/a
19	MXI1	chr3:48731851-48732819	IMR90	lung:	n/a	n/a
20	CEBPB	chr3:48732219-48732438	K562	blood:	n/a	chr3:48732320-48732331
21	NR3C1	chr3:48731447-48732286	A549	lung:	n/a	n/a
22	TCF12	chr3:48731825-48732655	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:48731964-48733172	GM12878	blood:	n/a	n/a
24	CEBPB	chr3:48732091-48732591	ECC-1	luminal epithelium:	n/a	chr3:48732320-48732331
25	POLR2A	chr3:48732202-48733042	GM12891	blood:	n/a	n/a
26	NR3C1	chr3:48731980-48732229	A549	lung:	n/a	n/a
27	POLR2A	chr3:48731983-48733135	U87	brain:	n/a	n/a
28	E2F4	chr3:48731963-48732538	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr3:48732095-48732533	MCF-7	breast:	n/a	chr3:48732320-48732331
30	CTCF	chr3:48732140-48732290	HBMEC	blood vessel:	n/a	n/a
31	FOSL1	chr3:48731835-48732475	HCT-116	colon:	n/a	n/a
32	CEBPB	chr3:48731959-48732563	HCT-116	colon:	n/a	chr3:48732320-48732331
33	MAZ	chr3:48732163-48732568	Hela-S3	cervix:	n/a	n/a
34	FOS	chr3:48731924-48732499	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr3:48732083-48733179	GM12878	blood:	n/a	n/a
36	FOS	chr3:48731928-48732343	MCF10A-Er-Src	breast:	n/a	n/a
37	NFIC	chr3:48732011-48732726	ECC-1	luminal epithelium:	n/a	n/a
38	CEBPB	chr3:48732201-48732436	A549	lung:	n/a	chr3:48732320-48732331
39	POLR2A	chr3:48732211-48733067	GM12891	blood:	n/a	n/a
40	TCF7L2	chr3:48732096-48732460	Hela-S3	cervix:	n/a	n/a
41	FOS	chr3:48731929-48732421	MCF10A-Er-Src	breast:	n/a	n/a
42	CEBPB	chr3:48731833-48732678	HCT-116	colon:	n/a	chr3:48732320-48732331
43	RCOR1	chr3:48732214-48732504	Hela-S3	cervix:	n/a	n/a
44	MYC	chr3:48732047-48732528	MCF10A-Er-Src	breast:	n/a	n/a
45	MYC	chr3:48731929-48732617	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:48732026-48732749	HUVEC	blood vessel:	n/a	n/a
47	NFIC	chr3:48731868-48732641	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr3:48732074-48733145	HepG2	liver:	n/a	n/a
49	MAZ	chr3:48731099-48733260	IMR90	lung:	n/a	n/a
50	CEBPB	chr3:48732124-48732525	ECC-1	luminal epithelium:	n/a	chr3:48732320-48732331

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48732213-48732263	GM12878	blood:	n/a
2	chr3:48732213-48732263	Hela-S3	cervix:	n/a
3	chr3:48732213-48732263	PANC-1	pancreas:	n/a
4	chr3:48732213-48732263	HUVEC	blood vessel:	n/a
5	chr3:48732213-48732263	HRE	kidney:	n/a
6	chr3:48732213-48732263	A549	lung:	n/a
7	chr3:48732213-48732263	SK-N-SH_RA	brain:	n/a
8	chr3:48732213-48732263	Hepatocyte	liver:	n/a
9	chr3:48732213-48732263	GM12892	blood:	n/a
10	chr3:48732213-48732263	HRPEpiC	eye:	n/a
11	chr3:48732213-48732263	AG04449	skin:	fetal
12	chr3:48732213-48732263	HL-60	blood:	n/a
13	chr3:48732213-48732263	SKMC	muscle:	n/a
14	chr3:48732213-48732263	PrEC	prostate:	n/a
15	chr3:48732213-48732263	GM12891	blood:	n/a
16	chr3:48732213-48732263	BE2_C	brain:	n/a
17	chr3:48732213-48732263	Caco-2	colon:	n/a
18	chr3:48732213-48732263	HCPEpiC	choroid plexus:	n/a
19	chr3:48732213-48732263	NB4	blood:	n/a
20	chr3:48732213-48732263	H1-hESC	embryonic stem cell:	embryo
21	chr3:48732213-48732263	HMEC	breast:	n/a
22	chr3:48732213-48732263	NHBE	bronchial:	n/a
23	chr3:48732213-48732263	AG04450	lung:	fetal
24	chr3:48732213-48732263	HCT-116	colon:	n/a
25	chr3:48732213-48732263	HRCEpiC	kidney:	n/a
26	chr3:48732213-48732263	SK-N-MC	brain:	n/a
27	chr3:48732213-48732263	GM06990	blood:	n/a
28	chr3:48732213-48732263	HEK293	kidney:	embryo
29	chr3:48732213-48732263	MCF10A-Er-Src	breast:	n/a
30	chr3:48732213-48732263	ovcar-3	ovarian:	n/a
31	chr3:48732213-48732263	HCF	heart:	n/a
32	chr3:48732213-48732263	SAEC	small airway:	n/a
33	chr3:48732213-48732263	HepG2	liver:	n/a
34	chr3:48732213-48732263	IMR90	lung:	fetal
35	chr3:48732213-48732263	AoSMC	blood vessel:	n/a
36	chr3:48732213-48732263	AG10803	skin:	n/a
37	chr3:48732213-48732263	NH-A	brain:	n/a
38	chr3:48732213-48732263	U87	brain:	n/a
39	chr3:48732213-48732263	ProgFib	skin:	n/a
40	chr3:48732213-48732263	MCF-7	breast:	n/a
41	chr3:48732213-48732263	PFSK-1	brain:	n/a
42	chr3:48732213-48732263	NT2-D1	testis:	n/a
43	chr3:48732213-48732263	HIPEpiC	eye:	n/a
44	chr3:48732213-48732263	Jurkat	blood:	n/a
45	chr3:48732213-48732263	ECC-1	luminal epithelium:	n/a
46	chr3:48732213-48732263	HEEpiC	esophagus:	n/a
47	chr3:48732213-48732263	GM19239	blood:	n/a
48	chr3:48732213-48732263	AG09319	gingival:	n/a
49	chr3:48732213-48732263	BJ	skin:	n/a
50	chr3:48732213-48732263	HAEpiC	amniotic membrane:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TREX1-2	chr3:48731727-48732701	ENSG00000232483

No data

Variant related genes	Relation type
IP6K2	TF binding region
IP6K2	CpG island
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000228350	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10865952	1.00[ASN][1000 genomes]
rs11706203	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708786	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715177	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes]
rs11719291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs12107418	0.81[EUR][1000 genomes]
rs12493578	1.00[ASN][1000 genomes]
rs12497850	1.00[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13063223	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324119	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324950	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13434258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1352420	0.90[ASN][1000 genomes]
rs17080319	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28452701	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28567949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28657585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28793701	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34096717	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34153629	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34577723	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35064573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3821875	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4077495	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858798	1.00[ASN][1000 genomes]
rs4858828	1.00[ASN][1000 genomes]
rs4858831	1.00[ASN][1000 genomes]
rs56735597	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61137521	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6768448	0.85[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	1.00[ASN][1000 genomes]
rs68042649	0.85[EUR][1000 genomes]
rs73078362	0.81[EUR][1000 genomes]
rs7633840	0.92[ASN][1000 genomes]
rs9809222	0.85[EUR][1000 genomes]
rs9811027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9811318	0.85[EUR][1000 genomes]
rs9812200	0.83[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821797	0.85[EUR][1000 genomes]
rs9834996	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836462	0.85[EUR][1000 genomes]
rs9841602	0.85[EUR][1000 genomes]
rs9848203	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9854034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873726	0.85[EUR][1000 genomes]
rs9877542	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877685	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882549	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11557629	WDR6	cis	lung	GTEx
rs11557629	WDR6	cis	Adipose Subcutaneous	GTEx
rs11557629	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11557629	WDR6	cis	Esophagus Mucosa	GTEx
rs11557629	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
5	chr3:48724600-48732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:48724600-48732400	Strong transcription	Fetal Intestine Large	intestine
7	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
8	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
11	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
13	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
14	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:48724800-48732400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr3:48724800-48732400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr3:48724800-48732400	Strong transcription	Colonic Mucosa	Colon
18	chr3:48724800-48732400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:48724800-48732400	Strong transcription	Fetal Intestine Small	intestine
20	chr3:48724800-48732400	Strong transcription	Gastric	stomach
21	chr3:48724800-48732400	Strong transcription	Lung	lung
22	chr3:48724800-48732600	Strong transcription	Spleen	Spleen
23	chr3:48724800-48732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:48724800-48733000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:48724800-48733000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:48724800-48733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:48724800-48733800	Strong transcription	HepG2	liver
28	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:48725000-48732400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:48725000-48732400	Strong transcription	Placenta	Placenta
34	chr3:48725000-48733200	Strong transcription	Liver	Liver
35	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:48725000-48740800	Strong transcription	Dnd41	blood
39	chr3:48725200-48732400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:48725200-48732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:48725200-48732800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:48725200-48733200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:48725400-48732400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:48725400-48733200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:48725800-48732400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:48725800-48732600	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:48726000-48732400	Strong transcription	Fetal Stomach	stomach
50	chr3:48727200-48733000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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