Variant report

Variant	rs12120414
Chromosome Location	chr1:56843129-56843130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:56841704-56843534	SK-N-SH	brain:	n/a	chr1:56841864-56841874
2	GATA3	chr1:56841709-56843612	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr1:56839169-56846366	SK-N-SH	brain:	n/a	chr1:56839904-56839918 chr1:56840249-56840261
4	EP300	chr1:56839159-56845078	SK-N-SH	brain:	n/a	chr1:56842588-56842595 chr1:56841267-56841281

Variant related genes	Relation type
ENSG00000223307	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10493205	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493206	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493207	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493208	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11206797	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12122982	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133160	0.90[AFR][1000 genomes]
rs12135065	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562368	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12732326	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732886	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12733519	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12734077	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1931076	0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4244023	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4244024	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344366	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4408191	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600084	0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4912229	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61772749	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671902	0.91[AFR][1000 genomes]
rs67708636	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12120414	DHCR24	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56839000-56845000	Enhancers	Fetal Muscle Leg	muscle
2	chr1:56839200-56846800	Enhancers	Fetal Stomach	stomach
3	chr1:56839400-56844600	Enhancers	Fetal Lung	lung
4	chr1:56839400-56844800	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:56839600-56843800	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr1:56839600-56844200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:56839600-56844800	Enhancers	Colon Smooth Muscle	Colon
8	chr1:56839800-56843800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:56839800-56844600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:56840000-56843400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:56840000-56843800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:56840000-56844800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:56840000-56862400	Weak transcription	Gastric	stomach
14	chr1:56840200-56843400	Weak transcription	Colonic Mucosa	Colon
15	chr1:56840200-56843600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:56840200-56843600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:56840200-56844400	Enhancers	Fetal Heart	heart
18	chr1:56840200-56845000	Enhancers	Brain Germinal Matrix	brain
19	chr1:56840400-56843200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:56840400-56843800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:56840400-56843800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:56840800-56843600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:56840800-56844400	Weak transcription	HepG2	liver
24	chr1:56841800-56843600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:56842000-56844600	Enhancers	Left Ventricle	heart
26	chr1:56842200-56843600	Enhancers	Right Atrium	heart
27	chr1:56842400-56844800	Enhancers	Brain Substantia Nigra	brain
28	chr1:56842400-56862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:56842600-56843600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:56842600-56843800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:56842600-56844000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr1:56842600-56844000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:56842600-56844200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:56842600-56844800	Enhancers	Brain Hippocampus Middle	brain
35	chr1:56842600-56849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:56842600-56850600	Weak transcription	NHDF-Ad	bronchial
37	chr1:56842600-56859800	Weak transcription	Right Ventricle	heart
38	chr1:56842800-56843200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:56842800-56843600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:56842800-56843800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:56842800-56843800	Weak transcription	Brain Angular Gyrus	brain
42	chr1:56842800-56844000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:56842800-56844000	Weak transcription	Fetal Brain Male	brain
44	chr1:56842800-56844000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:56842800-56844400	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:56842800-56844600	Weak transcription	Fetal Kidney	kidney
47	chr1:56842800-56848800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:56843000-56843400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:56843000-56843400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:56843000-56844400	Weak transcription	HMEC	breast

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