Variant report

Variant	rs12024187
Chromosome Location	chr1:155777840-155777841
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10908481	0.85[EUR][1000 genomes]
rs11264410	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264413	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12024257	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12040894	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12081192	0.85[EUR][1000 genomes]
rs12407800	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297775	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28582361	0.84[ASN][1000 genomes]
rs2985707	0.81[ASN][1000 genomes]
rs35698157	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4278368	0.85[EUR][1000 genomes]
rs6657670	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6662953	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs860295	0.81[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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872469	chr1:155743310-155810293	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12024187	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs12024187	RIT1	cis	Thyroid	GTEx
rs12024187	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12024187	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
6	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:155732200-155789200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:155746400-155791400	Weak transcription	Stomach Mucosa	stomach
10	chr1:155747600-155787200	Weak transcription	Esophagus	oesophagus
11	chr1:155747800-155785600	Weak transcription	Fetal Brain Male	brain
12	chr1:155747800-155791200	Weak transcription	Fetal Heart	heart
13	chr1:155748000-155789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155758800-155778400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:155760400-155779000	Strong transcription	Thymus	Thymus
16	chr1:155761600-155778400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:155762200-155798000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:155762600-155779200	Strong transcription	Fetal Stomach	stomach
19	chr1:155762600-155785000	Strong transcription	Fetal Intestine Small	intestine
20	chr1:155762800-155779200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:155763000-155779000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:155765200-155803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:155765200-155813200	Weak transcription	Psoas Muscle	Psoas
24	chr1:155766200-155782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:155767200-155779200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:155768600-155778600	Strong transcription	Primary T cells from cord blood	blood
27	chr1:155768600-155779000	Strong transcription	Dnd41	blood
28	chr1:155769800-155783400	Weak transcription	NHLF	lung
29	chr1:155771200-155783000	Weak transcription	A549	lung
30	chr1:155771400-155798400	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:155771600-155798200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:155772000-155798000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:155772200-155779200	Strong transcription	NH-A	brain
34	chr1:155772400-155785800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:155772600-155779200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:155773200-155778800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:155773200-155779000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:155773400-155779000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:155773400-155779000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:155773600-155779000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:155773800-155781200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:155773800-155787200	Weak transcription	Brain Substantia Nigra	brain
43	chr1:155774000-155778600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:155774400-155787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:155774600-155778800	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:155775000-155778200	Weak transcription	Fetal Brain Female	brain
47	chr1:155775000-155778400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:155775000-155778600	Weak transcription	K562	blood
49	chr1:155775000-155780600	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:155775000-155782000	Weak transcription	Rectal Smooth Muscle	rectum

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