Variant report

Variant	rs16866487
Chromosome Location	chr3:191057336-191057337
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191047482..191049844-chr3:191056418..191059474,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188958	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11542549	0.92[ASN][1000 genomes]
rs1435062	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520202	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520203	0.93[ASN][1000 genomes]
rs1609926	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16822378	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16822382	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16866504	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16866505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17753967	0.87[ASN][1000 genomes]
rs17810246	0.87[ASN][1000 genomes]
rs17810282	0.87[ASN][1000 genomes]
rs17838893	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056333	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364379	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28715898	0.87[ASN][1000 genomes]
rs3796219	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3959143	0.81[ASN][1000 genomes]
rs4677631	0.87[ASN][1000 genomes]
rs4677632	0.87[ASN][1000 genomes]
rs4677725	0.87[ASN][1000 genomes]
rs4677726	0.87[ASN][1000 genomes]
rs4677727	0.87[ASN][1000 genomes]
rs56174842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57211729	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58141749	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58645265	0.92[ASN][1000 genomes]
rs59709586	0.91[EUR][1000 genomes]
rs61250936	0.88[EUR][1000 genomes]
rs6444541	0.87[ASN][1000 genomes]
rs73185209	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73185210	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73185213	0.92[ASN][1000 genomes]
rs73185226	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73185228	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73185240	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73185255	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73185263	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73185284	0.91[EUR][1000 genomes]
rs73185287	0.91[EUR][1000 genomes]
rs73185288	0.91[EUR][1000 genomes]
rs73201627	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73201628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73201630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73201631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637196	0.87[ASN][1000 genomes]
rs7642387	0.87[ASN][1000 genomes]
rs7648886	0.87[ASN][1000 genomes]
rs9290986	0.87[ASN][1000 genomes]
rs9823680	0.87[ASN][1000 genomes]
rs9824437	0.87[ASN][1000 genomes]
rs9839751	0.83[ASN][1000 genomes]
rs9843934	0.87[ASN][1000 genomes]
rs9853569	0.87[ASN][1000 genomes]
rs9863255	0.89[ASN][1000 genomes]
rs9876944	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191049000-191058600	Weak transcription	Left Ventricle	heart
2	chr3:191049200-191060600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:191049400-191057600	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:191049800-191061600	Weak transcription	HSMMtube	muscle
5	chr3:191050200-191060200	Weak transcription	Psoas Muscle	Psoas
6	chr3:191050200-191074800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:191050600-191060400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:191050800-191057800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:191051200-191060200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:191051400-191057400	Weak transcription	Ovary	ovary
11	chr3:191051400-191058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:191051400-191059400	Weak transcription	Right Atrium	heart
13	chr3:191051400-191060000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:191051400-191060200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:191051400-191060200	Weak transcription	Right Ventricle	heart
16	chr3:191052200-191062400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:191052400-191057800	Enhancers	Hela-S3	cervix
18	chr3:191053200-191059200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:191053400-191057800	Enhancers	NHDF-Ad	bronchial
20	chr3:191053400-191058000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:191054200-191057400	Enhancers	NHLF	lung
22	chr3:191054600-191057800	Enhancers	Osteobl	bone
23	chr3:191054600-191058200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:191055000-191059200	Weak transcription	Adipose Nuclei	Adipose
25	chr3:191055200-191058000	Enhancers	NHEK	skin
26	chr3:191055400-191061800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:191055600-191057800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:191055600-191062000	Enhancers	HepG2	liver
29	chr3:191055800-191058400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:191056000-191057600	Enhancers	Primary B cells from cord blood	blood
31	chr3:191056000-191057600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr3:191056000-191058400	Enhancers	Fetal Heart	heart
33	chr3:191056000-191058400	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:191056000-191061000	Enhancers	Liver	Liver
35	chr3:191056200-191057400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:191056200-191057600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:191056200-191062200	Enhancers	Fetal Brain Male	brain
38	chr3:191056200-191063400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:191056400-191057400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:191056400-191057400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:191056400-191057400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:191056400-191057400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:191056400-191057400	Enhancers	GM12878-XiMat	blood
44	chr3:191056400-191057600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:191056400-191058000	Enhancers	HUVEC	blood vessel
46	chr3:191056400-191058400	Enhancers	Colon Smooth Muscle	Colon
47	chr3:191056400-191059200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:191056400-191060000	Weak transcription	HSMM	muscle
49	chr3:191056600-191059200	Weak transcription	A549	lung
50	chr3:191056800-191057800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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