Variant report

Variant	rs13155255
Chromosome Location	chr5:178038542-178038543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178035506..178039480-chr5:178042939..178045569,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11249553	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249554	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249556	0.82[EUR][1000 genomes]
rs11737903	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740194	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746942	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747742	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514311	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12518589	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156622	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs262027	0.90[CHB][hapmap]
rs35460909	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35522922	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36008351	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519984	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530542	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs555417	0.94[JPT][hapmap]
rs574103	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576097	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584415	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602019	0.97[ASN][1000 genomes]
rs602451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs643936	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs649585	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882079	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6886390	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721144	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7700943	0.82[CEU][hapmap]
rs7702727	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7724406	0.82[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][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	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13155255	CLK4	cis	normal skin	skin_eQTL
rs13155255	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
2	chr5:178022400-178038600	Weak transcription	Small Intestine	intestine
3	chr5:178023200-178046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:178024000-178050000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:178024400-178046000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:178026200-178050200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:178026400-178048400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr5:178026400-178050000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:178026400-178050200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:178026400-178050200	Strong transcription	Fetal Lung	lung
11	chr5:178026400-178050400	Strong transcription	Placenta	Placenta
12	chr5:178026400-178050400	Strong transcription	Fetal Thymus	thymus
13	chr5:178026400-178050400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:178026400-178050600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:178026400-178050800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:178026800-178050400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:178027000-178047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:178027000-178049800	Strong transcription	Dnd41	blood
19	chr5:178027000-178050600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:178027400-178049400	Strong transcription	GM12878-XiMat	blood
21	chr5:178027600-178050000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr5:178027600-178050400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr5:178028000-178050400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:178028000-178050400	Strong transcription	NH-A	brain
25	chr5:178028200-178046000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:178028200-178049600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:178028200-178050200	Strong transcription	Fetal Intestine Large	intestine
28	chr5:178028400-178046800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:178028400-178049800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:178028400-178050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:178028400-178050400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr5:178028600-178046200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:178028600-178046200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:178028800-178046000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:178028800-178050400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:178029000-178047200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:178029800-178041800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:178030200-178049800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:178030400-178050400	Strong transcription	HSMM	muscle
40	chr5:178030600-178050400	Strong transcription	Osteobl	bone
41	chr5:178030800-178039600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:178030800-178039800	Strong transcription	Brain Hippocampus Middle	brain
43	chr5:178030800-178040200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:178030800-178045800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:178031200-178041200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:178031800-178038800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:178031800-178041000	Weak transcription	Right Ventricle	heart
48	chr5:178031800-178046200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:178031800-178046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:178031800-178052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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