Variant report

Variant	rs10424652
Chromosome Location	chr19:55901310-55901311
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55900718..55902395-chr19:55953618..55955972,2	K562	blood:
2	chr19:55894730..55901388-chr19:55970612..55975937,9	K562	blood:
3	chr19:55724006..55730191-chr19:55893749..55903961,17	K562	blood:
4	chr19:55901176..55903609-chr19:56015366..56016869,2	K562	blood:
5	chr19:55791572..55793348-chr19:55900971..55904360,3	K562	blood:
6	chr19:55901062..55903652-chr19:55943271..55945381,2	K562	blood:
7	chr19:55723991..55730191-chr19:55895529..55902666,13	K562	blood:
8	chr19:55791572..55793348-chr19:55900971..55903516,2	K562	blood:
9	chr19:55765943..55767641-chr19:55900364..55902152,2	K562	blood:
10	chr19:55865353..55867670-chr19:55900964..55902717,2	K562	blood:
11	chr19:55828032..55829651-chr19:55900502..55903432,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000133265	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000187902	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10403564	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404049	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408088	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408448	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408525	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408540	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410269	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411984	0.90[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs10415365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416908	0.89[ASW][hapmap];1.00[CHB][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes]
rs10421889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423589	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425107	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425362	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425596	0.90[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs28408730	1.00[AFR][1000 genomes]
rs28536711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797308	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4252548	1.00[CHB][hapmap]
rs59698058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619651	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
7	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
8	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
9	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
10	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
11	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10424652	RPL28	cis	lymphoblastoid	seeQTL
rs10424652	RPL28	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55897600-55903000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:55897800-55901400	Transcr. at gene 5' and 3'	Hela-S3	cervix
3	chr19:55897800-55902200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:55897800-55903000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:55898000-55901400	Transcr. at gene 5' and 3'	K562	blood
6	chr19:55898000-55901800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:55898600-55902200	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr19:55898600-55902200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:55898800-55901800	Genic enhancers	Fetal Brain Male	brain
10	chr19:55898800-55903000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr19:55899000-55901400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
12	chr19:55899000-55901600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:55899000-55902200	Weak transcription	HSMMtube	muscle
14	chr19:55899000-55903000	Genic enhancers	Brain Angular Gyrus	brain
15	chr19:55899000-55903000	Genic enhancers	Fetal Muscle Leg	muscle
16	chr19:55899200-55901800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:55899200-55902200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:55899200-55902200	Genic enhancers	Spleen	Spleen
19	chr19:55899200-55903000	Genic enhancers	Pancreas	Pancrea
20	chr19:55899200-55903400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr19:55899200-55913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:55899400-55902000	Genic enhancers	H1 Cell Line	embryonic stem cell
23	chr19:55899400-55902000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:55899400-55902800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr19:55899400-55903000	Genic enhancers	Gastric	stomach
26	chr19:55899400-55903000	Genic enhancers	NHDF-Ad	bronchial
27	chr19:55899400-55903400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr19:55899600-55901400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:55899600-55901600	Genic enhancers	Lung	lung
30	chr19:55899600-55901800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:55899600-55902200	Genic enhancers	Colonic Mucosa	Colon
32	chr19:55899600-55902400	Strong transcription	Aorta	Aorta
33	chr19:55899600-55902600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:55899600-55903000	Genic enhancers	Brain Inferior Temporal Lobe	brain
35	chr19:55899600-55903600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:55899600-55904400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:55899800-55901400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:55899800-55901600	Strong transcription	Fetal Kidney	kidney
39	chr19:55899800-55903000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:55900000-55901400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:55900000-55901400	Genic enhancers	Esophagus	oesophagus
42	chr19:55900000-55901400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr19:55900000-55901800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:55900000-55902000	Strong transcription	Ovary	ovary
45	chr19:55900000-55902200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:55900000-55902200	Genic enhancers	Brain Hippocampus Middle	brain
47	chr19:55900000-55902400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:55900000-55902800	Genic enhancers	Right Ventricle	heart
49	chr19:55900000-55902800	Genic enhancers	HepG2	liver
50	chr19:55900000-55903000	Strong transcription	Fetal Lung	lung

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