Variant report

Variant	rs17086801
Chromosome Location	chr4:57337528-57337529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
2	chr4:57333435..57335762-chr4:57336689..57342030,5	MCF-7	breast:
3	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
4	chr4:57335761..57337736-chr4:57343152..57345663,2	MCF-7	breast:
5	chr4:57333514..57335901-chr4:57336352..57338475,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1140982	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1142851	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934479	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940993	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640212	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643989	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12643996	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649799	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134963	0.84[JPT][hapmap]
rs1579019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086759	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086773	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086830	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086868	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086898	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086909	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086919	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086922	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2176785	0.84[JPT][hapmap]
rs2271924	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34398021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34419325	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733324	0.81[JPT][hapmap]
rs3733326	0.85[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796539	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796540	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796549	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796550	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128534	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs41498446	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4631106	0.84[JPT][hapmap]
rs55778537	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55890437	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55903333	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55909588	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56129706	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56296497	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56362514	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57245446	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58654038	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59153415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59686671	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59764923	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59828502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830145	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831869	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7437839	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7658340	0.94[ASN][1000 genomes]
rs7688482	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086801	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57337800	Weak transcription	Esophagus	oesophagus
2	chr4:57334800-57337800	Weak transcription	Gastric	stomach
3	chr4:57334800-57337800	Weak transcription	Pancreas	Pancrea
4	chr4:57334800-57338000	Weak transcription	Lung	lung
5	chr4:57334800-57340200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57334800-57340200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:57334800-57340200	Weak transcription	Left Ventricle	heart
8	chr4:57334800-57340200	Weak transcription	Small Intestine	intestine
9	chr4:57334800-57340200	Weak transcription	Spleen	Spleen
10	chr4:57334800-57353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
13	chr4:57335000-57337600	Weak transcription	Ovary	ovary
14	chr4:57335000-57337800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:57335000-57337800	Weak transcription	Thymus	Thymus
16	chr4:57335000-57340200	Weak transcription	Aorta	Aorta
17	chr4:57335000-57340800	Weak transcription	Colonic Mucosa	Colon
18	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:57335200-57337800	Weak transcription	Brain Angular Gyrus	brain
20	chr4:57335200-57337800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:57335200-57337800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:57335200-57337800	Weak transcription	HSMMtube	muscle
23	chr4:57335200-57338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:57335200-57340200	Weak transcription	Psoas Muscle	Psoas
25	chr4:57335200-57340200	Weak transcription	Right Ventricle	heart
26	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:57335400-57337600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:57335400-57338600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:57335600-57337600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:57335600-57337600	Weak transcription	Fetal Brain Male	brain
31	chr4:57335600-57337600	Weak transcription	NHDF-Ad	bronchial
32	chr4:57335600-57337800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:57335600-57337800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:57335600-57337800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:57335600-57337800	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:57335600-57337800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:57335600-57338000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:57335600-57340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:57335800-57337800	Weak transcription	Brain Anterior Caudate	brain
41	chr4:57335800-57354800	Weak transcription	Fetal Heart	heart
42	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:57336000-57337800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:57336000-57337800	Weak transcription	Adipose Nuclei	Adipose
49	chr4:57336000-57337800	Weak transcription	Fetal Lung	lung
50	chr4:57336000-57337800	Weak transcription	Hela-S3	cervix

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