Variant report

Variant	rs12024257
Chromosome Location	chr1:155780536-155780537
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	chr1:155779007..155780786-chr1:155785874..155788055,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10796954	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264410	0.83[ASN][1000 genomes]
rs11264413	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12024187	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12040894	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407800	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1973768	0.92[ASN][1000 genomes]
rs28582361	0.86[ASN][1000 genomes]
rs2948072	0.81[ASN][1000 genomes]
rs2985707	0.83[ASN][1000 genomes]
rs35698157	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820594	0.81[AMR][1000 genomes]
rs6657670	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6662953	0.85[ASN][1000 genomes]
rs708611	0.80[ASN][1000 genomes]
rs822025	0.81[ASN][1000 genomes]
rs822478	0.82[ASN][1000 genomes]
rs860295	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	esv3397126	chr1:155778353-155781201	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3428267	chr1:155778603-155780751	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3357014	chr1:155779078-155780576	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12024257	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs12024257	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12024257	RIT1	cis	Thyroid	GTEx
rs12024257	FDPS	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	chr1:155762200-155798000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:155762600-155785000	Strong transcription	Fetal Intestine Small	intestine
16	chr1:155765200-155803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:155765200-155813200	Weak transcription	Psoas Muscle	Psoas
18	chr1:155766200-155782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:155769800-155783400	Weak transcription	NHLF	lung
20	chr1:155771200-155783000	Weak transcription	A549	lung
21	chr1:155771400-155798400	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:155771600-155798200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:155772000-155798000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:155772400-155785800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:155773800-155781200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:155773800-155787200	Weak transcription	Brain Substantia Nigra	brain
27	chr1:155774400-155787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:155775000-155780600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:155775000-155782000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:155775000-155782000	Weak transcription	HMEC	breast
31	chr1:155775000-155782600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:155775000-155782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:155775000-155782800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:155775000-155782800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:155775000-155783000	Weak transcription	Colonic Mucosa	Colon
36	chr1:155775000-155795600	Weak transcription	Small Intestine	intestine
37	chr1:155775200-155782600	Weak transcription	HUVEC	blood vessel
38	chr1:155775400-155783000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:155776000-155782400	Weak transcription	Ovary	ovary
40	chr1:155776000-155796600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:155776800-155782600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:155776800-155782800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:155777000-155780600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:155777000-155780600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:155777000-155780600	Weak transcription	GM12878-XiMat	blood
46	chr1:155777000-155782200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:155777000-155782600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:155777000-155782800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:155777000-155787200	Weak transcription	Pancreas	Pancrea
50	chr1:155777000-155787400	Weak transcription	Gastric	stomach

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