Variant report

Variant	rs13181921
Chromosome Location	chr5:178051375-178051376
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	MYC	chr5:178051369-178053564	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:178051355-178054657	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:178050980-178051634	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr5:178051322-178051553	K562	blood:	n/a	n/a
5	POLR2A	chr5:178051370-178051539	Hela-S3	cervix:	n/a	n/a
6	FOS	chr5:178051328-178052093	MCF10A-Er-Src	breast:	n/a	chr5:178051421-178051433 chr5:178051364-178051373
7	POLR2A	chr5:178051334-178054847	MCF10A-Er-Src	breast:	n/a	n/a
8	WRNIP1	chr5:178051166-178051652	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178029668..178031491-chr5:178050533..178053383,2	K562	blood:
2	chr5:178035433..178037862-chr5:178050507..178052447,2	K562	blood:
3	chr5:178019997..178022007-chr5:178050984..178053956,2	MCF-7	breast:
4	chr5:178049762..178051706-chr5:178156637..178158195,2	MCF-7	breast:
5	chr5:178050940..178053910-chr5:178263858..178266243,2	MCF-7	breast:
6	chr5:177650184..177652351-chr5:178050731..178052958,2	K562	blood:

Variant related genes	Relation type
RN7SKP70	TF binding region
CLK4	TF binding region
ENSG00000175309	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10063148	0.86[ASN][1000 genomes]
rs10066600	0.86[ASN][1000 genomes]
rs10070146	0.86[ASN][1000 genomes]
rs10070856	0.84[ASN][1000 genomes]
rs10464070	0.91[ASN][1000 genomes]
rs10479431	0.87[ASN][1000 genomes]
rs10479500	0.85[ASN][1000 genomes]
rs11747899	0.81[ASN][1000 genomes]
rs12054903	0.86[ASN][1000 genomes]
rs12188543	0.83[ASN][1000 genomes]
rs12189095	0.83[ASN][1000 genomes]
rs12234109	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs262023	0.88[ASN][1000 genomes]
rs262024	0.90[ASN][1000 genomes]
rs262029	0.81[ASN][1000 genomes]
rs262033	0.91[ASN][1000 genomes]
rs262041	0.81[ASN][1000 genomes]
rs262042	0.82[ASN][1000 genomes]
rs34183525	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34724127	0.86[ASN][1000 genomes]
rs35178365	0.83[ASN][1000 genomes]
rs35943178	0.83[ASN][1000 genomes]
rs3925517	0.84[ASN][1000 genomes]
rs4424014	0.83[ASN][1000 genomes]
rs4437395	0.83[ASN][1000 genomes]
rs4579274	0.83[ASN][1000 genomes]
rs540371	0.82[ASN][1000 genomes]
rs543862	0.92[ASN][1000 genomes]
rs55724549	0.89[ASN][1000 genomes]
rs55783860	0.87[ASN][1000 genomes]
rs57862544	0.95[ASN][1000 genomes]
rs62392801	0.87[ASN][1000 genomes]
rs6884172	0.95[ASN][1000 genomes]
rs6884657	0.95[ASN][1000 genomes]
rs71611451	0.86[ASN][1000 genomes]
rs71611452	0.86[ASN][1000 genomes]
rs7447517	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700943	0.91[ASN][1000 genomes]
rs7724406	0.91[ASN][1000 genomes]
rs9329047	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13181921	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	chr5:178031800-178052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178035800-178052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:178042200-178051400	Weak transcription	Pancreas	Pancrea
4	chr5:178043400-178051400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:178044000-178051400	Weak transcription	Fetal Intestine Small	intestine
6	chr5:178044000-178052000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:178044000-178052000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:178047000-178051600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:178047000-178052000	Weak transcription	Esophagus	oesophagus
10	chr5:178047000-178052200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:178047200-178051400	Weak transcription	Gastric	stomach
12	chr5:178047200-178052000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:178047400-178051400	Weak transcription	Spleen	Spleen
14	chr5:178047400-178052000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:178047400-178052000	Weak transcription	Lung	lung
16	chr5:178047600-178051800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:178048200-178051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:178048400-178051600	Weak transcription	Colonic Mucosa	Colon
19	chr5:178049800-178051400	Enhancers	Fetal Heart	heart
20	chr5:178050000-178051400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:178050000-178051400	Enhancers	Brain Angular Gyrus	brain
22	chr5:178050000-178051400	Enhancers	Brain Anterior Caudate	brain
23	chr5:178050000-178051400	Enhancers	Brain Germinal Matrix	brain
24	chr5:178050200-178051400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:178050200-178051400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:178050200-178051400	Weak transcription	Fetal Intestine Large	intestine
27	chr5:178050200-178051400	Weak transcription	A549	lung
28	chr5:178050200-178051600	Genic enhancers	Primary B cells from cord blood	blood
29	chr5:178050200-178051600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:178050200-178051800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:178050200-178052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:178050400-178051400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:178050400-178051400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:178050400-178051400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr5:178050400-178051400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:178050400-178051400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:178050400-178051400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr5:178050400-178051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:178050400-178051400	Enhancers	Liver	Liver
40	chr5:178050400-178051400	Weak transcription	Left Ventricle	heart
41	chr5:178050400-178051400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:178050400-178051400	Weak transcription	HMEC	breast
43	chr5:178050400-178051400	Enhancers	NHDF-Ad	bronchial
44	chr5:178050400-178051600	Active TSS	GM12878-XiMat	blood
45	chr5:178050400-178051800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:178050400-178051800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:178050400-178052000	Weak transcription	Placenta	Placenta
48	chr5:178050600-178051400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:178050600-178051400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:178050600-178052000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links