Variant report

Variant	rs12507723
Chromosome Location	chr4:54218086-54218087
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54212699..54214471-chr4:54216075..54218598,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10012853	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10013573	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10028214	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1014056	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10517291	0.84[ASN][1000 genomes]
rs10517292	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10517296	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11133267	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11935822	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11942086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946199	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11947322	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12499401	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12501431	0.81[EUR][1000 genomes]
rs13120051	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13125807	0.82[EUR][1000 genomes]
rs13130836	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1351514	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082659	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082910	0.82[EUR][1000 genomes]
rs2128103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170421	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271555	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271557	0.82[EUR][1000 genomes]
rs2292579	0.82[EUR][1000 genomes]
rs34028346	0.82[EUR][1000 genomes]
rs34173240	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34317954	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35033239	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35089532	0.82[EUR][1000 genomes]
rs35225781	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35313782	0.82[EUR][1000 genomes]
rs3817270	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3946758	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3986364	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4385131	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4864753	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6420001	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6554095	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554096	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554102	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554103	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6554107	0.82[EUR][1000 genomes]
rs6554108	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6846569	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847289	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71597836	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72498838	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7678953	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7679743	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7684450	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7684894	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7694840	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs980988	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs997832	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9992820	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9997358	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9997844	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12507723	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:54188200-54218200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54201200-54220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:54202200-54226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:54206600-54220200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:54210400-54225600	Weak transcription	Small Intestine	intestine
8	chr4:54211400-54219200	Weak transcription	Fetal Intestine Small	intestine
9	chr4:54211600-54219600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:54211600-54220200	Weak transcription	Fetal Stomach	stomach
11	chr4:54212000-54220600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:54212000-54227200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:54212200-54220800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:54212600-54219200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:54212800-54219600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:54213200-54220200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:54213600-54228600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:54213800-54218600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:54213800-54230400	Weak transcription	Fetal Kidney	kidney
20	chr4:54214000-54218600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:54214000-54218800	Weak transcription	Adipose Nuclei	Adipose
22	chr4:54214000-54219200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:54214000-54221800	Weak transcription	Ovary	ovary
24	chr4:54214000-54230800	Weak transcription	Aorta	Aorta
25	chr4:54214000-54231200	Weak transcription	Lung	lung
26	chr4:54214200-54218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:54214200-54218400	Weak transcription	Primary B cells from cord blood	blood
28	chr4:54214200-54218600	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:54214200-54218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:54214200-54218800	Weak transcription	Gastric	stomach
31	chr4:54214200-54218800	Weak transcription	Left Ventricle	heart
32	chr4:54214200-54218800	Weak transcription	NHLF	lung
33	chr4:54214200-54219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:54214200-54219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:54214200-54220200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:54214200-54221800	Weak transcription	Pancreas	Pancrea
37	chr4:54214200-54221800	Weak transcription	Psoas Muscle	Psoas
38	chr4:54214200-54224000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:54214200-54228200	Weak transcription	Esophagus	oesophagus
40	chr4:54214200-54228200	Weak transcription	Fetal Brain Female	brain
41	chr4:54214200-54228200	Weak transcription	NH-A	brain
42	chr4:54214200-54228800	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:54214200-54229000	Weak transcription	HUVEC	blood vessel
44	chr4:54214200-54230000	Weak transcription	Fetal Heart	heart
45	chr4:54214200-54230000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:54214200-54230400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:54214200-54230800	Weak transcription	Brain Angular Gyrus	brain
48	chr4:54214200-54230800	Weak transcription	Brain Substantia Nigra	brain
49	chr4:54214200-54230800	Weak transcription	Fetal Lung	lung
50	chr4:54214200-54230800	Weak transcription	Right Ventricle	heart

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