Variant report

Variant	rs530542
Chromosome Location	chr5:178022626-178022627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178022246..178024591-chr5:178025333..178028233,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10063220	0.82[ASN][1000 genomes]
rs11249553	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249554	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737903	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs11740194	0.87[EUR][1000 genomes]
rs11746942	0.87[EUR][1000 genomes]
rs11747742	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs12514311	0.86[EUR][1000 genomes]
rs12518589	0.86[EUR][1000 genomes]
rs13155255	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13156622	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs262027	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs35460909	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35522922	0.83[EUR][1000 genomes]
rs36008351	0.86[EUR][1000 genomes]
rs3925518	0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4079110	0.80[ASN][1000 genomes]
rs4587090	0.80[ASN][1000 genomes]
rs4976738	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs501721	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs519984	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs543862	0.82[CEU][hapmap]
rs555417	0.90[MEX][hapmap]
rs574103	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs576097	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs584415	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs596780	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602019	0.89[ASN][1000 genomes]
rs602451	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes]
rs643936	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649585	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865775	0.82[ASN][1000 genomes]
rs6882079	0.82[EUR][1000 genomes]
rs6883747	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6886390	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6890632	0.82[ASN][1000 genomes]
rs721144	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7700943	0.82[CEU][hapmap]
rs7702727	0.87[EUR][1000 genomes]
rs7724406	0.82[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs9329045	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv883216	chr5:178002325-178025087	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs530542	CLK4	cis	normal skin	skin_eQTL
rs530542	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs530542	CLK4	cis	cerebellum	SCAN
rs530542	FLT4	cis	parietal	SCAN
rs530542	CLK4	cis	lesional skin	skin_eQTL
rs530542	RUFY1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017800-178023200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
3	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
4	chr5:178017800-178033400	Weak transcription	Gastric	stomach
5	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
6	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
7	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
11	chr5:178018400-178023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:178018400-178024200	Weak transcription	Osteobl	bone
13	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
15	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:178018800-178024600	Weak transcription	Left Ventricle	heart
17	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:178019200-178024200	Weak transcription	Fetal Thymus	thymus
20	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
21	chr5:178019600-178027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:178020600-178028000	Weak transcription	NHLF	lung
23	chr5:178021200-178023200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr5:178021200-178023600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr5:178021200-178024000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:178021400-178023200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
27	chr5:178021400-178024000	Weak transcription	Thymus	Thymus
28	chr5:178021400-178024400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:178021400-178024400	Weak transcription	Fetal Intestine Small	intestine
30	chr5:178021400-178024400	Weak transcription	Lung	lung
31	chr5:178021400-178025200	Weak transcription	Spleen	Spleen
32	chr5:178021600-178022800	Weak transcription	HSMM	muscle
33	chr5:178021600-178024000	Weak transcription	Fetal Stomach	stomach
34	chr5:178021600-178031200	Weak transcription	Ovary	ovary
35	chr5:178021800-178022800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr5:178021800-178023200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr5:178021800-178023200	ZNF genes & repeats	Fetal Lung	lung
38	chr5:178021800-178023600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:178021800-178024600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:178021800-178024600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:178021800-178026800	Weak transcription	A549	lung
42	chr5:178022000-178023200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
43	chr5:178022000-178023600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:178022000-178023600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr5:178022000-178023600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr5:178022000-178030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:178022200-178023000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr5:178022200-178023200	ZNF genes & repeats	Liver	Liver
49	chr5:178022200-178023600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:178022400-178022800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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