Variant report

Variant	rs17086794
Chromosome Location	chr4:57334752-57334753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57274956..57277925-chr4:57332751..57335099,2	MCF-7	breast:
2	chr4:57251940..57255035-chr4:57332077..57334754,4	MCF-7	breast:
3	chr4:57334621..57337468-chr4:57366931..57368856,2	K562	blood:
4	chr4:57331783..57334990-chr4:57394745..57398997,7	K562	blood:
5	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
6	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
7	chr4:57334099..57335760-chr4:57411009..57413881,2	K562	blood:
8	chr4:57110581..57112837-chr4:57332810..57334755,2	K562	blood:
9	chr4:57332264..57334926-chr4:57844078..57846239,2	MCF-7	breast:
10	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
11	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
12	chr4:57333087..57335313-chr4:57842375..57845002,3	K562	blood:
13	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
14	chr4:57333435..57335762-chr4:57336689..57342030,5	MCF-7	breast:
15	chr4:57334260..57336507-chr4:57410772..57412509,2	K562	blood:
16	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
17	chr4:57333899..57336357-chr4:57340358..57342235,2	MCF-7	breast:
18	chr4:57332142..57335262-chr4:57394352..57398997,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000109265	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10008223	0.85[ASN][1000 genomes]
rs10013402	0.87[ASN][1000 genomes]
rs10017460	0.86[ASN][1000 genomes]
rs10051	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10434444	0.88[ASN][1000 genomes]
rs10434445	0.85[ASN][1000 genomes]
rs1060472	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11133442	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12498340	0.83[ASN][1000 genomes]
rs12501334	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12503412	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12504291	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12505767	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12505939	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508008	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12509542	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12510712	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12511770	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12513091	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646890	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs14211	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474179	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17086696	0.87[ASN][1000 genomes]
rs17086832	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17086853	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967559	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1983378	0.88[ASN][1000 genomes]
rs2030366	0.88[ASN][1000 genomes]
rs28510634	0.85[ASN][1000 genomes]
rs28866881	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4340842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4346704	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4618376	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864579	0.87[ASN][1000 genomes]
rs4864580	0.87[ASN][1000 genomes]
rs4864583	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4864585	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865092	0.89[ASN][1000 genomes]
rs4865103	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865107	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865108	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5010012	0.85[ASN][1000 genomes]
rs55915354	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56040009	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56099714	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56229630	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56392224	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56887793	0.89[ASN][1000 genomes]
rs58151706	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58333131	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554358	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66858948	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66863699	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820314	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6821301	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6824893	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829250	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6832797	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6834696	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6849183	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664841	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7670991	0.83[ASN][1000 genomes]
rs8340	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17086794	SRP72	cis	Whole Blood	GTEx
rs17086794	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs17086794	SRP72	cis	Esophagus Mucosa	GTEx
rs17086794	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs17086794	SRP72	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57331400-57334800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr4:57331600-57335000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:57331800-57334800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:57331800-57335200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr4:57331800-57335600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:57332000-57334800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:57332000-57334800	Active TSS	Fetal Kidney	kidney
8	chr4:57332000-57335000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:57332000-57335000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:57332000-57335200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:57332000-57335200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:57332000-57335800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:57332200-57334800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr4:57332200-57335000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:57332200-57335200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:57332200-57335800	Active TSS	K562	blood
17	chr4:57332400-57334800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:57332400-57334800	Active TSS	Fetal Intestine Small	intestine
19	chr4:57332400-57334800	Active TSS	Gastric	stomach
20	chr4:57332400-57334800	Active TSS	Pancreas	Pancrea
21	chr4:57332400-57334800	Active TSS	HSMMtube	muscle
22	chr4:57332400-57335000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:57332400-57335000	Active TSS	Aorta	Aorta
24	chr4:57332400-57335000	Active TSS	Colonic Mucosa	Colon
25	chr4:57332400-57335000	Active TSS	HMEC	breast
26	chr4:57332400-57335200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:57332400-57335200	Active TSS	GM12878-XiMat	blood
28	chr4:57332400-57335400	Active TSS	A549	lung
29	chr4:57332400-57335400	Active TSS	NHLF	lung
30	chr4:57332400-57335800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:57332400-57335800	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr4:57332600-57334800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:57332600-57334800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:57332600-57334800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:57332600-57334800	Active TSS	Esophagus	oesophagus
36	chr4:57332600-57334800	Active TSS	Fetal Muscle Trunk	muscle
37	chr4:57332600-57334800	Active TSS	Fetal Stomach	stomach
38	chr4:57332600-57334800	Active TSS	Left Ventricle	heart
39	chr4:57332600-57334800	Active TSS	Lung	lung
40	chr4:57332600-57334800	Active TSS	NHEK	skin
41	chr4:57332600-57335000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:57332600-57335000	Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:57332600-57335000	Active TSS	Ovary	ovary
44	chr4:57332600-57335000	Active TSS	NHDF-Ad	bronchial
45	chr4:57332600-57335200	Active TSS	Fetal Intestine Large	intestine
46	chr4:57332600-57335200	Active TSS	Psoas Muscle	Psoas
47	chr4:57332600-57335200	Active TSS	Right Ventricle	heart
48	chr4:57332600-57335200	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr4:57332600-57335400	Active TSS	HSMM	muscle
50	chr4:57332800-57334800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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