Variant report

Variant	rs11249554
Chromosome Location	chr5:178053487-178053488
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	ZNF384	chr5:178052770-178054463	K562	blood:	n/a	n/a
2	USF2	chr5:178053452-178053608	Hela-S3	cervix:	n/a	n/a
3	PBX3	chr5:178053344-178053830	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:178053049-178054494	GM19099	blood:	n/a	n/a
5	YY1	chr5:178053290-178054169	GM12892	blood:	n/a	chr5:178054040-178054054 chr5:178054038-178054049 chr5:178054020-178054042 chr5:178054032-178054042 chr5:178054032-178054042 chr5:178054031-178054039
6	SMC3	chr5:178053135-178054427	Hela-S3	cervix:	n/a	chr5:178053454-178053464
7	RUNX3	chr5:178053104-178054187	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:178053171-178054584	Hela-S3	cervix:	n/a	n/a
9	BHLHE40	chr5:178052939-178054553	GM12878	blood:	n/a	chr5:178054543-178054552 chr5:178053688-178053704 chr5:178054544-178054553 chr5:178054544-178054553
10	REST	chr5:178053410-178054201	HL-60	blood:	n/a	chr5:178053678-178053691
11	MYC	chr5:178052572-178054553	K562	blood:	n/a	chr5:178054227-178054237 chr5:178054223-178054233 chr5:178054544-178054553 chr5:178054333-178054340
12	RELA	chr5:178053313-178054213	GM12892	blood:	n/a	chr5:178053518-178053527 chr5:178053518-178053527
13	ETS1	chr5:178053409-178054194	K562	blood:	n/a	n/a
14	POLR2A	chr5:178053380-178054426	GM10847	blood:	n/a	n/a
15	TAF1	chr5:178053444-178054173	GM12892	blood:	n/a	n/a
16	POLR2A	chr5:178053190-178054319	K562	blood:	n/a	n/a
17	MYC	chr5:178051369-178053564	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:178053284-178053518	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:178053108-178054454	K562	blood:	n/a	n/a
20	RUNX3	chr5:178053311-178054207	GM12878	blood:	n/a	n/a
21	TAF1	chr5:178053165-178054219	H1-neurons	neurons:	n/a	n/a
22	TBL1XR1	chr5:178053274-178054539	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:178052968-178054585	H1-neurons	neurons:	n/a	n/a
24	CBX3	chr5:178053388-178054227	K562	blood:	n/a	n/a
25	EP300	chr5:178053362-178054183	HepG2	liver:	n/a	n/a
26	TCF12	chr5:178053319-178054222	A549	lung:	n/a	chr5:178053550-178053558 chr5:178053881-178053888
27	POLR2A	chr5:178053265-178054482	ECC-1	luminal epithelium:	n/a	n/a
28	RFX5	chr5:178053426-178054196	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:178053048-178053801	HepG2	liver:	n/a	n/a
30	TAF1	chr5:178053349-178054328	ECC-1	luminal epithelium:	n/a	n/a
31	TAF1	chr5:178053398-178054220	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr5:178053350-178054184	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr5:178053265-178054273	H1-hESC	embryonic stem cell:	n/a	n/a
34	CREB1	chr5:178053316-178054434	HepG2	liver:	n/a	n/a
35	REST	chr5:178053358-178053831	PFSK-1	brain:	n/a	chr5:178053678-178053691
36	POLR2A	chr5:178052757-178054569	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:178053394-178054441	MCF-7	breast:	n/a	n/a
38	FOSL1	chr5:178053349-178053843	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr5:178052765-178054366	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:178052453-178054216	K562	blood:	n/a	n/a
41	POLR2A	chr5:178053144-178054193	GM12878	blood:	n/a	n/a
42	SP1	chr5:178053205-178054248	A549	lung:	n/a	chr5:178054145-178054154 chr5:178054143-178054155 chr5:178054218-178054227 chr5:178054226-178054238 chr5:178053444-178053458 chr5:178054228-178054237 chr5:178054226-178054238 chr5:178054227-178054237 chr5:178054143-178054155 chr5:178054227-178054236
43	HCFC1	chr5:178053469-178054626	K562	blood:	n/a	n/a
44	CEBPB	chr5:178053061-178054351	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:178053276-178054189	GM12891	blood:	n/a	n/a
46	POLR2A	chr5:178052889-178054181	PANC-1	pancreas:	n/a	n/a
47	STAT3	chr5:178053277-178054480	MCF10A-Er-Src	breast:	n/a	chr5:178054223-178054235 chr5:178054217-178054229 chr5:178054219-178054231
48	TEAD4	chr5:178052664-178054262	K562	blood:	n/a	n/a
49	SIN3AK20	chr5:178052863-178054455	MCF-7	breast:	n/a	n/a
50	UBTF	chr5:178053059-178054461	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:178053470-178053520	HPAEpiC	pulmonary alveolar:	n/a
2	chr5:178053470-178053520	GM12891	blood:	n/a
3	chr5:178053470-178053520	K562	blood:	n/a
4	chr5:178053470-178053520	RPTEC	kidney:	n/a
5	chr5:178053470-178053520	AG09319	gingival:	n/a
6	chr5:178053470-178053520	NT2-D1	testis:	n/a
7	chr5:178053470-178053520	HCT-116	colon:	n/a
8	chr5:178053470-178053520	LNCaP	prostate:	n/a
9	chr5:178053470-178053520	SAEC	small airway:	n/a
10	chr5:178053470-178053520	Caco-2	colon:	n/a
11	chr5:178053470-178053520	Jurkat	blood:	n/a
12	chr5:178053470-178053520	HCF	heart:	n/a
13	chr5:178053470-178053520	HEK293	kidney:	embryo
14	chr5:178053470-178053520	GM12892	blood:	n/a
15	chr5:178053470-178053520	A549	lung:	n/a
16	chr5:178053470-178053520	ovcar-3	ovarian:	n/a
17	chr5:178053470-178053520	HL-60	blood:	n/a
18	chr5:178053470-178053520	AG09309	skin:	n/a
19	chr5:178053470-178053520	HMEC	breast:	n/a
20	chr5:178053470-178053520	NHDF-neo	bronchial:	n/a
21	chr5:178053470-178053520	Hepatocyte	liver:	n/a
22	chr5:178053470-178053520	PFSK-1	brain:	n/a
23	chr5:178053470-178053520	U87	brain:	n/a
24	chr5:178053470-178053520	NH-A	brain:	n/a
25	chr5:178053470-178053520	NB4	blood:	n/a
26	chr5:178053470-178053520	AoSMC	blood vessel:	n/a
27	chr5:178053470-178053520	HIPEpiC	eye:	n/a
28	chr5:178053470-178053520	CMK	blood:	n/a
29	chr5:178053470-178053520	MCF10A-Er-Src	breast:	n/a
30	chr5:178053470-178053520	Hela-S3	cervix:	n/a
31	chr5:178053470-178053520	AG04450	lung:	fetal
32	chr5:178053470-178053520	HAEpiC	amniotic membrane:	n/a
33	chr5:178053470-178053520	T-47D	breast:	n/a
34	chr5:178053470-178053520	GM12878	blood:	n/a
35	chr5:178053470-178053520	GM06990	blood:	n/a
36	chr5:178053470-178053520	HCPEpiC	choroid plexus:	n/a
37	chr5:178053470-178053520	HepG2	liver:	n/a
38	chr5:178053470-178053520	HRCEpiC	kidney:	n/a
39	chr5:178053470-178053520	SK-N-SH	brain:	n/a
40	chr5:178053470-178053520	SK-N-SH_RA	brain:	n/a
41	chr5:178053470-178053520	HRPEpiC	eye:	n/a
42	chr5:178053470-178053520	HUVEC	blood vessel:	n/a
43	chr5:178053470-178053520	HNPCEpiC	eye:	n/a
44	chr5:178053470-178053520	AG10803	skin:	n/a
45	chr5:178053470-178053520	HEEpiC	esophagus:	n/a
46	chr5:178053470-178053520	MCF-7	breast:	n/a
47	chr5:178053470-178053520	SKMC	muscle:	n/a
48	chr5:178053470-178053520	HRE	kidney:	n/a
49	chr5:178053470-178053520	AG04449	skin:	fetal
50	chr5:178053470-178053520	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr5:178052822..178055819-chr5:178156143..178158096,2	MCF-7	breast:
2	chr5:178052987..178056050-chr5:178056072..178058258,3	MCF-7	breast:
3	chr5:177631376..177633067-chr5:178051942..178054079,2	K562	blood:
4	chr5:178017082..178020481-chr5:178051764..178053531,4	MCF-7	breast:
5	chr5:178019997..178022007-chr5:178050984..178053956,2	MCF-7	breast:
6	chr5:178053026..178055082-chr6:26156240..26159025,2	MCF-7	breast:
7	chr5:178051446..178054153-chr5:178157357..178158910,2	MCF-7	breast:
8	chr5:178050940..178053910-chr5:178263858..178266243,2	MCF-7	breast:
9	chr5:178053433..178053933-chrX:41193160..41193798,2	Hela-S3	cervix:
10	chr5:177659087..177660769-chr5:178052015..178054177,2	K562	blood:
11	chr5:177631162..177632942-chr5:178051796..178054079,4	K562	blood:
12	chr5:178053391..178055177-chr5:178285758..178288394,2	MCF-7	breast:

Variant related genes	Relation type
CLK4	TF binding region
CLK4	CpG island
ENSG00000050767	Chromatin interaction
ENSG00000175309	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000169131	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000215301	Chromatin interaction
ENSG00000113240	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11249553	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249556	0.84[EUR][1000 genomes]
rs11737903	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740194	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11746942	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11747742	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12514311	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12518589	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13155255	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13156622	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35460909	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35522922	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36008351	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs501721	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519984	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs530542	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs574103	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576097	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584415	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596780	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602019	0.93[ASN][1000 genomes]
rs602451	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643936	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs649585	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882079	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6886390	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721144	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7702727	0.92[EUR][1000 genomes];0.94[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3342261	chr5:178053396-178055344	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11249554	CLK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178051000-178054400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:178051000-178054600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr5:178051200-178054600	Active TSS	Aorta	Aorta
4	chr5:178051400-178054400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:178051600-178054400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:178051600-178054600	Active TSS	NHDF-Ad	bronchial
7	chr5:178051600-178054600	Active TSS	NHLF	lung
8	chr5:178051800-178054600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:178051800-178054600	Active TSS	HSMM	muscle
10	chr5:178051800-178054800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:178052000-178054200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:178052000-178054200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:178052000-178054400	Active TSS	Fetal Intestine Large	intestine
14	chr5:178052000-178054400	Active TSS	Lung	lung
15	chr5:178052000-178054600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:178052000-178054600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:178052000-178054600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:178052000-178054600	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr5:178052000-178054800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:178052000-178054800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:178052000-178054800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:178052200-178054000	Bivalent/Poised TSS	HepG2	liver
24	chr5:178052200-178054400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:178052200-178054400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:178052200-178054400	Active TSS	HMEC	breast
27	chr5:178052200-178054600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:178052200-178054600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr5:178052200-178054600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:178052200-178054600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:178052200-178054600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:178052200-178054600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:178052200-178054600	Active TSS	Esophagus	oesophagus
34	chr5:178052200-178054600	Active TSS	Fetal Heart	heart
35	chr5:178052200-178054600	Active TSS	Fetal Intestine Small	intestine
36	chr5:178052200-178054600	Active TSS	Fetal Kidney	kidney
37	chr5:178052200-178054800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:178052200-178054800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr5:178052200-178054800	Active TSS	Brain Anterior Caudate	brain
40	chr5:178052200-178054800	Active TSS	Colonic Mucosa	Colon
41	chr5:178052200-178054800	Active TSS	Colon Smooth Muscle	Colon
42	chr5:178052200-178054800	Active TSS	Fetal Brain Female	brain
43	chr5:178052200-178054800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr5:178052200-178054800	Active TSS	NH-A	brain
45	chr5:178052200-178054800	Active TSS	NHEK	skin
46	chr5:178052200-178054800	Active TSS	Osteobl	bone
47	chr5:178052400-178054200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:178052400-178054400	Active TSS	Primary T cells fromperipheralblood	blood
49	chr5:178052400-178054400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr5:178052400-178054400	Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links