Variant report

Variant	rs28670976
Chromosome Location	chr3:105180707-105180708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105179946..105182536-chr3:105183412..105185840,2	MCF-7	breast:
2	chr3:105084736..105086274-chr3:105179763..105181298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10049426	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036582	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036583	0.81[EUR][1000 genomes]
rs10511243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10933816	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10933817	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488994	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491980	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494392	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695118	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13062366	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13064396	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092811	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13093663	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13097669	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100098	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438538	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438541	0.94[ASN][1000 genomes]
rs1530069	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898654	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164956	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178407	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2196745	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2399045	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2895299	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426702	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4894831	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57834585	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437587	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437589	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66805489	0.81[EUR][1000 genomes]
rs6767277	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767814	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769302	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779807	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780238	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796658	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6806304	0.92[ASN][1000 genomes]
rs7431531	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615005	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629589	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644273	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647011	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649033	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288802	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934856	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975574	0.92[ASN][1000 genomes]
rs9842028	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851952	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883620	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883799	0.85[EUR][1000 genomes];0.97[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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
2	chr3:105167800-105185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:105175200-105184800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:105175400-105184400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105179000-105185000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:105179000-105191400	Weak transcription	HSMM	muscle
7	chr3:105179000-105192200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:105179200-105182000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:105179200-105184000	Weak transcription	NHDF-Ad	bronchial
10	chr3:105179200-105185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:105179600-105184200	Weak transcription	Liver	Liver
12	chr3:105179600-105184600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:105179600-105192400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:105180200-105184000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:105180200-105184000	Weak transcription	Osteobl	bone
16	chr3:105180400-105184000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:105180400-105184400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:105180600-105182000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:105180600-105184000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:105180600-105184200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:105180600-105185000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:105180600-105185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:105180600-105185400	Weak transcription	Brain Angular Gyrus	brain

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