Variant report

Variant	rs519984
Chromosome Location	chr5:178027236-178027237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178026410..178028805-chr5:178033864..178036012,2	K562	blood:
2	chr5:178026187..178028267-chr5:178030915..178032717,2	K562	blood:
3	chr5:178024210..178026391-chr5:178026680..178028373,2	K562	blood:
4	chr5:178022246..178024591-chr5:178025333..178028233,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11249553	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737903	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740194	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11746942	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747742	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12514311	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12518589	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13155255	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13156622	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs262027	0.80[ASN][1000 genomes]
rs35460909	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35522922	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36008351	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501721	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530542	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs574103	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576097	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584415	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs602019	0.99[ASN][1000 genomes]
rs602451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628857	0.86[AMR][1000 genomes]
rs643936	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649585	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882079	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6886390	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702727	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7732660	0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs519984	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
8	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
9	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
14	chr5:178020600-178028000	Weak transcription	NHLF	lung
15	chr5:178021600-178031200	Weak transcription	Ovary	ovary
16	chr5:178022000-178030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:178022400-178030800	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:178022400-178038600	Weak transcription	Small Intestine	intestine
19	chr5:178022600-178031000	Weak transcription	Right Ventricle	heart
20	chr5:178022800-178031600	Weak transcription	Fetal Brain Male	brain
21	chr5:178023000-178028000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:178023200-178027400	Weak transcription	Liver	Liver
23	chr5:178023200-178027600	Weak transcription	Brain Anterior Caudate	brain
24	chr5:178023200-178028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:178023200-178029000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:178023200-178030800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:178023200-178046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:178023400-178027400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:178023400-178027600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:178023400-178028000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:178023400-178028600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:178023400-178029400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:178023600-178028000	Weak transcription	NH-A	brain
34	chr5:178023600-178028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:178023600-178028800	Weak transcription	Brain Substantia Nigra	brain
36	chr5:178023600-178029600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:178023600-178029600	Weak transcription	Brain Germinal Matrix	brain
38	chr5:178023600-178029800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:178023600-178030800	Weak transcription	Fetal Kidney	kidney
40	chr5:178023600-178031000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:178023800-178028600	Weak transcription	Fetal Brain Female	brain
42	chr5:178023800-178028800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:178024000-178050000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:178024200-178030000	Strong transcription	Osteobl	bone
45	chr5:178024200-178031000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:178024400-178031200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:178024400-178046000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:178024600-178028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:178024600-178031000	Weak transcription	Colonic Mucosa	Colon
50	chr5:178024600-178035800	Strong transcription	Primary B cells from cord blood	blood

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