Variant report

Variant	rs17082453
Chromosome Location	chr4:54011603-54011604
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	chr4:54007557..54010483-chr4:54011201..54014968,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11133246	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11133247	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11737703	1.00[YRI][hapmap]
rs11929903	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs11939189	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs12108246	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs12499016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507228	0.84[AMR][1000 genomes]
rs12512359	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12640471	0.84[AMR][1000 genomes]
rs12650397	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17082476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17082504	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17082529	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17082565	0.85[CHB][hapmap]
rs1987028	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2001881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4421047	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs4515221	0.84[AMR][1000 genomes]
rs4864451	0.85[CHB][hapmap]
rs4864453	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4864747	0.85[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs6826467	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs72624192	0.87[AMR][1000 genomes]
rs72624193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72624194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143456	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73143458	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73143484	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs751265	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs7688646	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap]
rs7696426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17082453	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53987800-54016800	Weak transcription	NHLF	lung
2	chr4:53993800-54027800	Weak transcription	Fetal Stomach	stomach
3	chr4:53995200-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:53995400-54017800	Weak transcription	Brain Substantia Nigra	brain
5	chr4:53997000-54017600	Weak transcription	Gastric	stomach
6	chr4:53997400-54020000	Weak transcription	HSMM	muscle
7	chr4:53998600-54014400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:53999000-54013200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:53999000-54017200	Weak transcription	Fetal Lung	lung
10	chr4:53999000-54027800	Weak transcription	NHDF-Ad	bronchial
11	chr4:54001200-54017600	Weak transcription	Spleen	Spleen
12	chr4:54003400-54019000	Weak transcription	GM12878-XiMat	blood
13	chr4:54003600-54012800	Weak transcription	Esophagus	oesophagus
14	chr4:54004000-54017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:54004200-54020800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:54005400-54012400	Weak transcription	HMEC	breast
18	chr4:54005600-54023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:54005800-54012800	Weak transcription	Fetal Brain Female	brain
20	chr4:54007000-54017600	Weak transcription	Right Ventricle	heart
21	chr4:54007200-54030600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:54008200-54017200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:54008200-54017600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:54008400-54013000	Weak transcription	Thymus	Thymus
25	chr4:54008600-54019000	Weak transcription	Fetal Intestine Small	intestine
26	chr4:54008800-54017400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:54009200-54017200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:54009400-54016400	Weak transcription	Placenta	Placenta
29	chr4:54009400-54017400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:54009600-54017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:54009600-54017600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:54009600-54017600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:54009600-54024000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:54009800-54011800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:54009800-54011800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:54009800-54011800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:54009800-54012400	Weak transcription	Small Intestine	intestine
38	chr4:54009800-54017800	Weak transcription	Colonic Mucosa	Colon
39	chr4:54010000-54012400	Weak transcription	Fetal Thymus	thymus
40	chr4:54010200-54011800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:54010200-54011800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:54010200-54011800	Strong transcription	Osteobl	bone
43	chr4:54010200-54034600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:54010600-54011800	Strong transcription	Primary T cells from cord blood	blood
45	chr4:54010800-54011800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:54010800-54011800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:54011000-54011800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:54011000-54011800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:54011000-54011800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:54011000-54011800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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