Variant report

Variant	rs17082581
Chromosome Location	chr4:54176763-54176764
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	chr4:54174793..54178568-chr4:54179278..54182842,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10517279	0.85[JPT][hapmap]
rs10517291	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]
rs10517292	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11930070	1.00[CEU][hapmap]
rs11947322	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947928	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12499016	1.00[CHB][hapmap]
rs12499731	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500564	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507228	0.81[AMR][1000 genomes]
rs12512748	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640471	0.81[AMR][1000 genomes]
rs17082529	0.81[AMR][1000 genomes]
rs17082549	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082565	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082579	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35784764	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4385131	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4515221	0.81[AMR][1000 genomes]
rs4864451	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864452	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864453	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864454	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864747	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864753	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6826467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830879	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6854446	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72498838	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73147378	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73147396	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73149212	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751265	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664488	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7664645	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7687029	0.88[AMR][1000 genomes]
rs9762074	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17082581	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54140200-54179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:54164400-54177400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:54168200-54188000	Weak transcription	Left Ventricle	heart
4	chr4:54169200-54180000	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:54169200-54187800	Weak transcription	Liver	Liver
6	chr4:54169400-54178600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:54169400-54187400	Weak transcription	Dnd41	blood
8	chr4:54169600-54187800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:54169800-54181400	Weak transcription	Fetal Lung	lung
10	chr4:54169800-54181400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:54169800-54187800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:54170000-54181400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:54170000-54183800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:54170000-54186800	Weak transcription	HSMM	muscle
16	chr4:54170600-54187600	Weak transcription	K562	blood
17	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:54170800-54181400	Weak transcription	Fetal Thymus	thymus
19	chr4:54171200-54179200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:54171200-54188000	Weak transcription	Esophagus	oesophagus
21	chr4:54171600-54181200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:54171600-54181400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:54171600-54181400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:54171600-54187600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:54171800-54177600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:54171800-54181400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:54172000-54181200	Weak transcription	Fetal Intestine Small	intestine
28	chr4:54172000-54188000	Weak transcription	Pancreas	Pancrea
29	chr4:54172000-54188000	Weak transcription	HepG2	liver
30	chr4:54172200-54180800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:54172200-54181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:54172600-54215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:54173000-54187600	Weak transcription	Brain Anterior Caudate	brain
34	chr4:54173200-54177800	Weak transcription	Gastric	stomach
35	chr4:54173200-54182000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:54173400-54181400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:54173400-54186800	Weak transcription	NH-A	brain
38	chr4:54173600-54182200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:54173800-54181800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:54174200-54177600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:54174200-54177600	Enhancers	NHDF-Ad	bronchial
42	chr4:54174200-54178200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:54174200-54181400	Weak transcription	Primary T cells from cord blood	blood
44	chr4:54174200-54187200	Weak transcription	Adipose Nuclei	Adipose
45	chr4:54174200-54187400	Weak transcription	A549	lung
46	chr4:54174200-54212600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:54174400-54177800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:54174600-54178400	Weak transcription	Primary B cells from cord blood	blood
49	chr4:54174600-54179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:54174800-54181600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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