Variant report

Variant	rs2023493
Chromosome Location	chr6:28400162-28400163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28392901..28395106-chr6:28398520..28400756,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1005125	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1016069	0.81[ASN][1000 genomes]
rs1052215	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946954	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150705	0.81[EUR][1000 genomes]
rs1150707	0.82[EUR][1000 genomes]
rs1150709	0.81[EUR][1000 genomes]
rs1150716	0.85[EUR][1000 genomes]
rs1233713	0.82[EUR][1000 genomes]
rs1361387	0.82[AMR][1000 genomes]
rs1736891	0.80[EUR][1000 genomes]
rs2108927	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs213232	0.87[EUR][1000 genomes]
rs213236	0.94[EUR][1000 genomes]
rs213237	0.94[EUR][1000 genomes]
rs213238	0.87[EUR][1000 genomes]
rs213240	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2142730	0.85[EUR][1000 genomes]
rs2191035	0.84[ASN][1000 genomes]
rs2247002	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531805	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2531806	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2531825	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531831	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2859348	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2859365	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4455662	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7206	0.82[EUR][1000 genomes]
rs728122	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs853684	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs916403	0.82[AMR][1000 genomes]
rs9301	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9368565	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468372	0.84[EUR][1000 genomes]

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2023493	AL022393.7	cis	lung	GTEx
rs2023493	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs2023493	AL022393.7	cis	Artery Tibial	GTEx
rs2023493	ZSCAN23	cis	Artery Tibial	GTEx
rs2023493	ZSCAN31	cis	lung	GTEx
rs2023493	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2023493	ZSCAN31	cis	Thyroid	GTEx
rs2023493	ZSCAN31	cis	Muscle Skeletal	GTEx
rs2023493	ZSCAN31	cis	Stomach	GTEx
rs2023493	AL022393.7	cis	Muscle Skeletal	GTEx
rs2023493	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2023493	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2023493	AL022393.7	cis	Nerve Tibial	GTEx
rs2023493	AL022393.7	cis	Artery Aorta	GTEx
rs2023493	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2023493	RP5-874C20.3	cis	Thyroid	GTEx
rs2023493	ZSCAN23	cis	lung	GTEx
rs2023493	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2023493	ZSCAN23	cis	Muscle Skeletal	GTEx
rs2023493	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2023493	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
4	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:28385600-28410800	Weak transcription	Lung	lung
6	chr6:28386000-28402200	Weak transcription	Osteobl	bone
7	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
11	chr6:28389200-28410200	Weak transcription	NHLF	lung
12	chr6:28389400-28403200	Weak transcription	Adipose Nuclei	Adipose
13	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
19	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:28391400-28402400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:28391400-28410400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:28391400-28410800	Weak transcription	Placenta	Placenta
23	chr6:28391600-28401800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:28391600-28402000	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:28391600-28402000	Weak transcription	Left Ventricle	heart
26	chr6:28391600-28402000	Weak transcription	Psoas Muscle	Psoas
27	chr6:28391600-28402200	Weak transcription	HSMMtube	muscle
28	chr6:28391600-28402200	Weak transcription	NH-A	brain
29	chr6:28391600-28410200	Weak transcription	Brain Anterior Caudate	brain
30	chr6:28391600-28410800	Weak transcription	Pancreas	Pancrea
31	chr6:28392000-28410200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:28392000-28410400	Weak transcription	NHEK	skin
33	chr6:28392200-28402000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:28392200-28410400	Weak transcription	Right Ventricle	heart
35	chr6:28392400-28410000	Weak transcription	HMEC	breast
36	chr6:28392400-28410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:28393600-28410800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:28393800-28402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:28393800-28404200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:28393800-28410600	Weak transcription	Aorta	Aorta
41	chr6:28394000-28401800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:28394200-28409800	Weak transcription	Fetal Heart	heart
43	chr6:28394400-28405000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28394800-28402000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:28395200-28401000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:28395200-28402200	Weak transcription	Primary T cells from cord blood	blood
47	chr6:28395200-28403800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:28395200-28410200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:28395400-28409400	Weak transcription	Fetal Brain Male	brain
50	chr6:28395800-28400800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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