Variant report

Variant	rs12971639
Chromosome Location	chr19:36617106-36617107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36583233..36586201-chr19:36617082..36618818,2	K562	blood:
2	chr19:36615077..36620423-chr19:36622100..36624907,6	K562	blood:
3	chr19:36610352..36613134-chr19:36616460..36619107,3	K562	blood:
4	chr19:36616979..36620071-chr19:36629993..36632800,4	K562	blood:

Variant related genes	Relation type
ENSG00000126247	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10418079	0.93[EUR][1000 genomes]
rs10420345	0.88[EUR][1000 genomes]
rs10422055	0.87[EUR][1000 genomes]
rs11879369	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12971936	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12972828	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12981698	0.95[EUR][1000 genomes]
rs2023866	0.81[EUR][1000 genomes]
rs2074435	0.88[EUR][1000 genomes]
rs2227260	0.88[EUR][1000 genomes]
rs2231568	0.89[EUR][1000 genomes]
rs3810447	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4806262	0.87[EUR][1000 genomes]
rs4806273	0.88[EUR][1000 genomes]
rs8104047	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104053	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12971639	POLR2I///RPSA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36607200-36618600	Weak transcription	Psoas Muscle	Psoas
2	chr19:36607400-36617200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr19:36607400-36618400	Weak transcription	Stomach Mucosa	stomach
4	chr19:36607400-36618600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:36607400-36618800	Weak transcription	Small Intestine	intestine
6	chr19:36607600-36617200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:36607600-36617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:36607600-36617200	Strong transcription	Placenta	Placenta
9	chr19:36607600-36618400	Weak transcription	K562	blood
10	chr19:36608000-36617200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:36608000-36617200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:36608000-36617200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:36608000-36617200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:36608000-36617200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:36608000-36617200	Strong transcription	Adipose Nuclei	Adipose
16	chr19:36608000-36617200	Strong transcription	Spleen	Spleen
17	chr19:36608000-36617200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:36608000-36617800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:36608000-36618000	Strong transcription	Fetal Stomach	stomach
20	chr19:36608200-36617200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:36608200-36617200	Strong transcription	A549	lung
22	chr19:36608200-36618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:36608800-36617200	Strong transcription	Gastric	stomach
24	chr19:36609000-36617200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr19:36609000-36617200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:36609000-36617200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:36609000-36617200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:36609200-36617200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:36609800-36617200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:36611200-36617200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36611400-36617200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:36611400-36617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:36611400-36617400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:36611600-36617200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr19:36611600-36618000	Strong transcription	Fetal Intestine Small	intestine
36	chr19:36611800-36617200	Strong transcription	Dnd41	blood
37	chr19:36612000-36617200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:36612600-36617200	Strong transcription	Liver	Liver
39	chr19:36612600-36618000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:36613600-36618400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:36614000-36617200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:36614000-36617400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:36614000-36618400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:36614200-36618800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:36615200-36618200	Weak transcription	Pancreas	Pancrea
46	chr19:36615200-36618400	Weak transcription	Primary B cells from cord blood	blood
47	chr19:36615200-36618400	Weak transcription	HUVEC	blood vessel
48	chr19:36615200-36618600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:36615400-36618600	Weak transcription	Fetal Brain Male	brain
50	chr19:36615800-36617200	Strong transcription	Brain Cingulate Gyrus	brain

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