Variant report

Variant	rs596780
Chromosome Location	chr5:178018665-178018666
allele	A/G
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	WRNIP1	chr5:178018594-178018691	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178017942..178020045-chr5:178023632..178025333,2	K562	blood:

Variant related genes	Relation type
COL23A1	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11249553	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11737903	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740194	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11746942	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747742	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12514311	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12518589	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13155255	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]
rs13156622	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs262027	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs35460909	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35522922	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36008351	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3925518	0.88[CHD][hapmap]
rs501721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530542	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs543862	0.82[CEU][hapmap]
rs555417	0.84[ASW][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs574103	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576097	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584415	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602019	1.00[ASN][1000 genomes]
rs602451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs643936	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6882079	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6886390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700943	0.82[CEU][hapmap]
rs7702727	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7724406	0.82[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs596780	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs596780	CLK4	cis	cerebellum	SCAN
rs596780	RMND5B	cis	cerebellum	SCAN
rs596780	FLT4	cis	parietal	SCAN
rs596780	CLK4	cis	normal skin	skin_eQTL
rs596780	CLK4	cis	lesional skin	skin_eQTL
rs596780	RUFY1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017600-178019000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr5:178017600-178021000	Weak transcription	Spleen	Spleen
3	chr5:178017800-178018800	Enhancers	Right Ventricle	heart
4	chr5:178017800-178019000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:178017800-178021000	Weak transcription	Lung	lung
6	chr5:178017800-178021200	Weak transcription	Ovary	ovary
7	chr5:178017800-178023200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
9	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
10	chr5:178017800-178033400	Weak transcription	Gastric	stomach
11	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
12	chr5:178018000-178018800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:178018000-178018800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:178018000-178021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:178018000-178021200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:178018000-178021200	Weak transcription	HSMM	muscle
17	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
18	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:178018200-178018800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:178018200-178018800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:178018200-178019000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:178018200-178019000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:178018200-178019400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:178018200-178021200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:178018200-178021200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:178018200-178021400	Weak transcription	Brain Substantia Nigra	brain
27	chr5:178018200-178021400	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:178018200-178021800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:178018200-178022000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:178018200-178022200	Weak transcription	Liver	Liver
31	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
34	chr5:178018400-178019000	Enhancers	HMEC	breast
35	chr5:178018400-178019000	Enhancers	NHEK	skin
36	chr5:178018400-178020800	Weak transcription	Fetal Stomach	stomach
37	chr5:178018400-178023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:178018400-178024200	Weak transcription	Osteobl	bone
39	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:178018600-178018800	Enhancers	Left Ventricle	heart
41	chr5:178018600-178018800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr5:178018600-178019400	Enhancers	Psoas Muscle	Psoas
43	chr5:178018600-178021400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:178018600-178021800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:178018600-178022000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
47	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links