Variant report

Variant	rs11942086
Chromosome Location	chr4:54220663-54220664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54220216..54222517-chr4:54223647..54225586,2	K562	blood:
2	chr4:54220179..54222765-chr4:54228443..54230623,2	K562	blood:
3	chr4:54215552..54217782-chr4:54219355..54221752,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10012853	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10013573	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10028214	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1014056	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10517291	0.82[ASN][1000 genomes]
rs10517292	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10517296	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133267	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935822	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946199	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11947322	0.82[AMR][1000 genomes]
rs12499401	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12507723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13120051	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13125807	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130836	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1351514	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082659	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082910	0.80[EUR][1000 genomes]
rs2128103	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2170421	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271555	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271557	0.80[EUR][1000 genomes]
rs2292579	0.80[EUR][1000 genomes]
rs34028346	0.80[EUR][1000 genomes]
rs34173240	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34317954	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35033239	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35089532	0.80[EUR][1000 genomes]
rs35225781	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35313782	0.80[EUR][1000 genomes]
rs3817270	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3946758	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3986364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4385131	0.82[AMR][1000 genomes]
rs4864753	0.82[AMR][1000 genomes]
rs6420001	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554095	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554096	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554102	0.82[ASN][1000 genomes]
rs6554103	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554107	0.81[EUR][1000 genomes]
rs6554108	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6846569	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847289	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71597836	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72498838	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7678953	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7679743	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7684450	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7684894	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7694840	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs980988	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9992820	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9997358	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9997844	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11942086	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:54202200-54226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:54210400-54225600	Weak transcription	Small Intestine	intestine
5	chr4:54212000-54227200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:54212200-54220800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:54213600-54228600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:54213800-54230400	Weak transcription	Fetal Kidney	kidney
9	chr4:54214000-54221800	Weak transcription	Ovary	ovary
10	chr4:54214000-54230800	Weak transcription	Aorta	Aorta
11	chr4:54214000-54231200	Weak transcription	Lung	lung
12	chr4:54214200-54221800	Weak transcription	Pancreas	Pancrea
13	chr4:54214200-54221800	Weak transcription	Psoas Muscle	Psoas
14	chr4:54214200-54224000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:54214200-54228200	Weak transcription	Esophagus	oesophagus
16	chr4:54214200-54228200	Weak transcription	Fetal Brain Female	brain
17	chr4:54214200-54228200	Weak transcription	NH-A	brain
18	chr4:54214200-54228800	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:54214200-54229000	Weak transcription	HUVEC	blood vessel
20	chr4:54214200-54230000	Weak transcription	Fetal Heart	heart
21	chr4:54214200-54230000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:54214200-54230400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:54214200-54230800	Weak transcription	Brain Angular Gyrus	brain
24	chr4:54214200-54230800	Weak transcription	Brain Substantia Nigra	brain
25	chr4:54214200-54230800	Weak transcription	Fetal Lung	lung
26	chr4:54214200-54230800	Weak transcription	Right Ventricle	heart
27	chr4:54214200-54230800	Weak transcription	HSMMtube	muscle
28	chr4:54214200-54231000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:54214200-54231000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:54214200-54231200	Weak transcription	Spleen	Spleen
31	chr4:54214400-54224400	Weak transcription	A549	lung
32	chr4:54214400-54230200	Weak transcription	HMEC	breast
33	chr4:54214600-54230000	Weak transcription	Brain Anterior Caudate	brain
34	chr4:54214800-54230200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:54215000-54226800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:54215800-54221200	Weak transcription	K562	blood
37	chr4:54216000-54221000	Weak transcription	HepG2	liver
38	chr4:54216000-54221200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:54216600-54227600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:54218200-54220800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:54218800-54220800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:54218800-54230800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:54219000-54224800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:54219000-54225800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:54219000-54227600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:54219000-54228400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:54219200-54221800	Weak transcription	NHDF-Ad	bronchial
48	chr4:54219200-54224800	Weak transcription	Osteobl	bone
49	chr4:54219200-54225800	Weak transcription	Dnd41	blood
50	chr4:54219200-54227400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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