Variant report

Variant	rs10012853
Chromosome Location	chr4:54250189-54250190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54248839..54251059-chr4:54253637..54255570,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10013573	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10028214	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1014056	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10517296	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935822	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946199	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12499401	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12501431	0.81[EUR][1000 genomes]
rs12507723	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13120051	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125807	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13130836	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351514	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17082659	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082910	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2128103	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170421	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271555	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271557	0.82[EUR][1000 genomes]
rs2292579	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34028346	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34173240	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34317954	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033239	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35089532	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35225781	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313782	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3817270	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3946758	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3986364	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6420001	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554095	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554096	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554102	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554103	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554107	0.82[EUR][1000 genomes]
rs6554108	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846569	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71597836	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678953	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679743	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684450	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684894	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694840	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992820	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997358	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9997844	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10012853	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54244600-54250200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:54244600-54250200	Weak transcription	Left Ventricle	heart
3	chr4:54244600-54256000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54244600-54256000	Weak transcription	Esophagus	oesophagus
5	chr4:54244600-54256000	Weak transcription	Gastric	stomach
6	chr4:54244600-54256000	Weak transcription	Lung	lung
7	chr4:54244600-54256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:54244600-54272800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:54244600-54310600	Weak transcription	Spleen	Spleen
10	chr4:54244600-54319200	Weak transcription	Pancreas	Pancrea
11	chr4:54244800-54250200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:54244800-54256000	Weak transcription	Stomach Mucosa	stomach
13	chr4:54245000-54252800	Weak transcription	Brain Angular Gyrus	brain
14	chr4:54245000-54271400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:54245200-54250200	Weak transcription	Fetal Stomach	stomach
16	chr4:54245200-54252800	Weak transcription	HSMMtube	muscle
17	chr4:54245400-54251800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:54245400-54253000	Weak transcription	Colonic Mucosa	Colon
19	chr4:54245400-54253000	Weak transcription	Psoas Muscle	Psoas
20	chr4:54245400-54256000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:54245400-54279400	Weak transcription	Right Ventricle	heart
22	chr4:54245600-54252800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:54245600-54269600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:54245600-54270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:54246000-54257800	Weak transcription	Fetal Heart	heart
26	chr4:54246000-54270200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:54246000-54270200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:54246200-54250600	Weak transcription	Brain Substantia Nigra	brain
29	chr4:54246200-54251600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:54246200-54252800	Weak transcription	Fetal Brain Female	brain
31	chr4:54246200-54252800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:54246200-54256000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:54246200-54256000	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:54246200-54276200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:54246200-54319200	Weak transcription	Aorta	Aorta
36	chr4:54246400-54250800	Weak transcription	Fetal Brain Male	brain
37	chr4:54246400-54251800	Weak transcription	Brain Anterior Caudate	brain
38	chr4:54246400-54255600	Weak transcription	Ovary	ovary
39	chr4:54246400-54259800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:54246400-54259800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr4:54246600-54250600	Weak transcription	NHEK	skin
42	chr4:54246600-54252600	Weak transcription	NHLF	lung
43	chr4:54246600-54253400	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:54246600-54255800	Weak transcription	Brain Germinal Matrix	brain
45	chr4:54246600-54259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:54246600-54270200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:54246600-54311200	Weak transcription	Small Intestine	intestine
48	chr4:54246800-54250600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:54246800-54250800	Weak transcription	Primary B cells from cord blood	blood
50	chr4:54246800-54252600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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