Variant report

Variant	rs262023
Chromosome Location	chr5:178025087-178025088
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	chr5:178017942..178020045-chr5:178023632..178025333,2	K562	blood:
2	chr5:178024210..178026391-chr5:178026680..178028373,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10464070	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10479431	0.80[ASN][1000 genomes]
rs10479500	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs11747742	0.82[CEU][hapmap]
rs11747899	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs12188543	0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs12189095	0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs12234109	0.98[ASN][1000 genomes]
rs13155255	0.82[CEU][hapmap]
rs13156622	0.81[CEU][hapmap]
rs13181921	0.88[ASN][1000 genomes]
rs262024	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262029	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs262033	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262041	0.88[ASN][1000 genomes]
rs262042	0.89[ASN][1000 genomes]
rs34183525	0.93[ASN][1000 genomes]
rs3925517	0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs501721	0.82[CEU][hapmap]
rs540371	0.89[ASN][1000 genomes]
rs543862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55724549	0.82[ASN][1000 genomes]
rs55783860	0.80[ASN][1000 genomes]
rs57862544	0.88[ASN][1000 genomes]
rs596780	0.82[CEU][hapmap]
rs602451	0.85[CEU][hapmap]
rs62392801	0.80[ASN][1000 genomes]
rs628857	0.81[CEU][hapmap]
rs6884172	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884657	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7447517	0.95[ASN][1000 genomes]
rs7700943	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7724406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732660	0.81[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs262023	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs262023	CLK4	cis	cerebellum	SCAN
rs262023	CLK4	cis	lesional skin	skin_eQTL
rs262023	FLT4	cis	parietal	SCAN
rs262023	RUFY1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
2	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
3	chr5:178017800-178033400	Weak transcription	Gastric	stomach
4	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
5	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
6	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
9	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
10	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
12	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
16	chr5:178019600-178027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:178020600-178028000	Weak transcription	NHLF	lung
18	chr5:178021400-178025200	Weak transcription	Spleen	Spleen
19	chr5:178021600-178031200	Weak transcription	Ovary	ovary
20	chr5:178021800-178026800	Weak transcription	A549	lung
21	chr5:178022000-178030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:178022400-178026000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:178022400-178030800	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:178022400-178038600	Weak transcription	Small Intestine	intestine
25	chr5:178022600-178031000	Weak transcription	Right Ventricle	heart
26	chr5:178022800-178031600	Weak transcription	Fetal Brain Male	brain
27	chr5:178023000-178026400	Weak transcription	HMEC	breast
28	chr5:178023000-178028000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:178023200-178026800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:178023200-178027000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:178023200-178027400	Weak transcription	Liver	Liver
32	chr5:178023200-178027600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:178023200-178028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:178023200-178029000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:178023200-178030800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:178023200-178046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:178023400-178025400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:178023400-178026400	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:178023400-178026800	Weak transcription	Primary T cells from cord blood	blood
40	chr5:178023400-178027400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:178023400-178027600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr5:178023400-178028000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:178023400-178028600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:178023400-178029400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:178023600-178025400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr5:178023600-178026200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:178023600-178026400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:178023600-178026400	Weak transcription	Adipose Nuclei	Adipose
49	chr5:178023600-178026400	Weak transcription	Fetal Lung	lung
50	chr5:178023600-178027200	Weak transcription	HSMM	muscle

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