Variant report

Variant	rs10517291
Chromosome Location	chr4:54215692-54215693
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	chr4:54215552..54217782-chr4:54219355..54221752,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10013573	0.86[CHB][hapmap]
rs1014056	0.85[CHB][hapmap]
rs10517292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10517296	0.85[CHB][hapmap]
rs11133267	0.85[CHB][hapmap]
rs11929903	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11930070	1.00[CEU][hapmap]
rs11935822	0.81[ASN][1000 genomes]
rs11939189	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11942086	0.82[ASN][1000 genomes]
rs11947322	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11947928	0.81[EUR][1000 genomes]
rs12108246	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs12499016	0.86[CHB][hapmap]
rs12499401	0.86[CHB][hapmap]
rs12499731	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12500564	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12507723	0.84[ASN][1000 genomes]
rs12512748	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120051	0.86[CHB][hapmap]
rs13125807	0.83[CHB][hapmap]
rs1351514	0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17082476	0.93[CHB][hapmap]
rs17082504	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs17082549	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17082565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17082579	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17082581	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17082910	0.86[CHB][hapmap]
rs1987028	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2128103	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2292579	0.86[CHB][hapmap]
rs35225781	0.85[CHB][hapmap]
rs35784764	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3817270	0.86[CHB][hapmap]
rs3946758	0.85[CHB][hapmap]
rs3986364	0.81[ASN][1000 genomes]
rs4385131	1.00[CEU][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4421047	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs4864451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864452	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864454	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864753	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6420001	0.85[CHB][hapmap]
rs6554095	0.82[ASN][1000 genomes]
rs6554096	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs6554108	0.85[CHB][hapmap]
rs6826467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6830879	0.82[EUR][1000 genomes]
rs6846569	0.81[ASN][1000 genomes]
rs6854446	0.82[EUR][1000 genomes]
rs72498838	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73147378	0.83[ASN][1000 genomes]
rs73147396	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73149212	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7664488	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7664645	0.81[EUR][1000 genomes]
rs7684450	0.86[CHB][hapmap]
rs7684894	0.81[ASN][1000 genomes]
rs7688646	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs9762074	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992820	0.85[CHB][hapmap]
rs9997844	0.85[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10517291	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:54188200-54218200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:54201200-54220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:54201800-54215800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:54202200-54226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54206600-54220200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:54210400-54225600	Weak transcription	Small Intestine	intestine
10	chr4:54211200-54216000	Weak transcription	Thymus	Thymus
11	chr4:54211400-54219200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:54211600-54219600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:54211600-54220200	Weak transcription	Fetal Stomach	stomach
14	chr4:54211800-54217800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:54212000-54220600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:54212000-54227200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:54212200-54220800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:54212400-54217800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:54212600-54219200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:54212800-54219600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:54213200-54220200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:54213400-54217200	Weak transcription	Liver	Liver
23	chr4:54213600-54216600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:54213600-54228600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:54213800-54218600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:54213800-54230400	Weak transcription	Fetal Kidney	kidney
27	chr4:54214000-54218600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:54214000-54218800	Weak transcription	Adipose Nuclei	Adipose
29	chr4:54214000-54219200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:54214000-54221800	Weak transcription	Ovary	ovary
31	chr4:54214000-54230800	Weak transcription	Aorta	Aorta
32	chr4:54214000-54231200	Weak transcription	Lung	lung
33	chr4:54214200-54216200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:54214200-54217400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:54214200-54218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:54214200-54218400	Weak transcription	Primary B cells from cord blood	blood
37	chr4:54214200-54218600	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:54214200-54218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:54214200-54218800	Weak transcription	Gastric	stomach
40	chr4:54214200-54218800	Weak transcription	Left Ventricle	heart
41	chr4:54214200-54218800	Weak transcription	NHLF	lung
42	chr4:54214200-54219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:54214200-54219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:54214200-54220200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:54214200-54221800	Weak transcription	Pancreas	Pancrea
46	chr4:54214200-54221800	Weak transcription	Psoas Muscle	Psoas
47	chr4:54214200-54224000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:54214200-54228200	Weak transcription	Esophagus	oesophagus
49	chr4:54214200-54228200	Weak transcription	Fetal Brain Female	brain
50	chr4:54214200-54228200	Weak transcription	NH-A	brain

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