Variant report

Variant	rs17082081
Chromosome Location	chr4:53692125-53692126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53582665..53585471-chr4:53689497..53692252,2	K562	blood:
2	chr4:53577830..53580008-chr4:53690583..53692647,2	MCF-7	breast:
3	chr4:53577643..53580213-chr4:53690826..53692756,2	K562	blood:
4	chr4:53689894..53692436-chr4:53702334..53704274,2	MCF-7	breast:
5	chr4:53690322..53693293-chr4:53696846..53698754,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226950	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10000595	0.86[EUR][1000 genomes]
rs10001855	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10008073	0.87[CEU][hapmap];0.93[CHB][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012770	0.90[EUR][1000 genomes]
rs10014464	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025825	0.90[EUR][1000 genomes]
rs10026175	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs10028558	0.90[EUR][1000 genomes]
rs10028567	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs1043975	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047959	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11934293	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11941562	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483685	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483686	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1483687	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082143	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17082147	0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17613967	0.90[EUR][1000 genomes]
rs1963003	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017237	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2046364	0.80[ASN][1000 genomes]
rs2062253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2200226	0.82[ASN][1000 genomes]
rs2279334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306601	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2411259	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs28419463	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28446124	0.89[EUR][1000 genomes]
rs28454903	0.92[EUR][1000 genomes]
rs28489424	0.92[EUR][1000 genomes]
rs28494193	0.82[EUR][1000 genomes]
rs28526700	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28609158	0.90[EUR][1000 genomes]
rs28704139	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733375	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28735908	0.92[EUR][1000 genomes]
rs28740880	0.90[EUR][1000 genomes]
rs28811693	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898676	0.90[EUR][1000 genomes]
rs2898677	0.90[EUR][1000 genomes]
rs2898681	0.86[JPT][hapmap]
rs301135	0.80[AMR][1000 genomes]
rs301136	0.80[AMR][1000 genomes]
rs4242020	0.92[EUR][1000 genomes]
rs4309903	0.92[EUR][1000 genomes]
rs4318712	0.90[EUR][1000 genomes]
rs4864673	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864679	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864681	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4864682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4864683	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864688	0.80[ASN][1000 genomes]
rs4864690	0.81[JPT][hapmap]
rs4864691	0.86[JPT][hapmap]
rs4865421	0.83[EUR][1000 genomes]
rs4865422	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4990628	0.92[EUR][1000 genomes]
rs5012592	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs55657347	0.90[EUR][1000 genomes]
rs57615871	0.90[EUR][1000 genomes]
rs59649036	0.80[ASN][1000 genomes]
rs61034963	0.83[EUR][1000 genomes]
rs61268502	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62336785	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336788	0.85[EUR][1000 genomes]
rs62336791	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62336792	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62336794	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62336795	0.81[ASN][1000 genomes]
rs62338801	0.92[EUR][1000 genomes]
rs62338805	0.92[EUR][1000 genomes]
rs6839084	0.86[JPT][hapmap]
rs6852148	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs73143042	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73248698	0.81[EUR][1000 genomes]
rs900607	0.81[ASN][1000 genomes]
rs922932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs922933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9646	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9993034	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53688600-53692400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:53688600-53692400	Enhancers	NHDF-Ad	bronchial
3	chr4:53688600-53692600	Enhancers	HMEC	breast
4	chr4:53688800-53692200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:53688800-53692400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:53688800-53692400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:53688800-53692600	Enhancers	Ovary	ovary
8	chr4:53689000-53692600	Enhancers	Placenta	Placenta
9	chr4:53689000-53693000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:53689200-53692200	Enhancers	NH-A	brain
11	chr4:53689200-53692200	Enhancers	NHLF	lung
12	chr4:53689200-53692600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:53689400-53692200	Enhancers	Fetal Stomach	stomach
14	chr4:53689400-53693000	Enhancers	Fetal Heart	heart
15	chr4:53689600-53692200	Enhancers	Right Ventricle	heart
16	chr4:53690000-53692400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:53690000-53692400	Enhancers	Gastric	stomach
18	chr4:53690000-53693000	Enhancers	Fetal Muscle Leg	muscle
19	chr4:53690400-53692400	Enhancers	Fetal Muscle Trunk	muscle
20	chr4:53690400-53692400	Enhancers	Psoas Muscle	Psoas
21	chr4:53690600-53692400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:53690600-53692600	Enhancers	Pancreas	Pancrea
23	chr4:53690600-53693000	Enhancers	Fetal Kidney	kidney
24	chr4:53690800-53692200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:53691000-53692600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr4:53691200-53692800	Enhancers	Dnd41	blood
27	chr4:53691200-53698800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:53691400-53692200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:53691400-53692200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:53691400-53692400	Enhancers	Primary T cells from cord blood	blood
31	chr4:53691400-53692400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr4:53691400-53692400	Enhancers	Fetal Thymus	thymus
33	chr4:53691400-53692600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:53691400-53692800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:53691400-53693200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:53691600-53692400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:53691600-53692400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:53691600-53692400	Enhancers	NHEK	skin
39	chr4:53691600-53698600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:53691600-53698800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:53691800-53692400	Enhancers	HepG2	liver
42	chr4:53691800-53692800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:53691800-53698800	Weak transcription	Left Ventricle	heart
44	chr4:53691800-53704000	Weak transcription	Right Atrium	heart

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