Variant report

Variant	rs6780633
Chromosome Location	chr3:196254970-196254971
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196253926..196256027-chr3:196295277..196297106,2	K562	blood:

Variant related genes	Relation type
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11185544	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706197	0.84[ASN][1000 genomes]
rs11711594	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711952	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714694	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920455	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489885	0.95[ASN][1000 genomes]
rs12490276	0.81[ASN][1000 genomes]
rs12494859	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495687	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054748	0.84[ASN][1000 genomes]
rs2054749	0.84[ASN][1000 genomes]
rs2054750	0.84[ASN][1000 genomes]
rs2086891	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101285	0.88[EUR][1000 genomes]
rs2341334	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341399	0.82[EUR][1000 genomes]
rs28479172	0.84[ASN][1000 genomes]
rs2880030	0.84[ASN][1000 genomes]
rs3964310	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488870	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144237	0.97[ASN][1000 genomes]
rs57365032	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60668021	0.84[ASN][1000 genomes]
rs62410583	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583317	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583318	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66588136	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6765975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6775806	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780856	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799694	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6799697	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6803397	0.92[ASN][1000 genomes]
rs6803596	0.87[ASN][1000 genomes]
rs6807081	0.89[ASN][1000 genomes]
rs6807097	0.92[ASN][1000 genomes]
rs6810083	0.89[ASN][1000 genomes]
rs73219653	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219654	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219660	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614249	0.86[ASN][1000 genomes]
rs7615547	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623111	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623224	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629990	0.92[ASN][1000 genomes]
rs7651365	0.86[ASN][1000 genomes]
rs9311	0.84[ASN][1000 genomes]
rs9647412	0.84[ASN][1000 genomes]
rs9647413	0.84[ASN][1000 genomes]
rs9811428	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9813420	0.84[ASN][1000 genomes]
rs9814342	0.84[ASN][1000 genomes]
rs9817377	0.84[ASN][1000 genomes]
rs9818507	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831225	0.84[ASN][1000 genomes]
rs9839347	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840938	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848622	0.88[EUR][1000 genomes]
rs9849530	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854347	0.90[ASN][1000 genomes]
rs9858251	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868492	0.84[ASN][1000 genomes]
rs9870613	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9880563	0.83[EUR][1000 genomes];0.95[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	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196254400-196255000	Flanking Active TSS	GM12878-XiMat	blood
2	chr3:196254400-196255000	Flanking Active TSS	K562	blood
3	chr3:196254400-196255400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:196254400-196255400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:196254400-196255400	Enhancers	Fetal Thymus	thymus
6	chr3:196254400-196255400	Enhancers	NHLF	lung
7	chr3:196254600-196255200	Enhancers	NHDF-Ad	bronchial
8	chr3:196254600-196255400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:196254600-196255400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:196254600-196255400	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:196254600-196255400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:196254600-196255400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:196254600-196255400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:196254600-196255400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:196254600-196255400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:196254600-196255400	Enhancers	Thymus	Thymus
17	chr3:196254600-196255400	Enhancers	Hela-S3	cervix
18	chr3:196254600-196255400	Enhancers	HMEC	breast
19	chr3:196254600-196255400	Enhancers	NH-A	brain
20	chr3:196254600-196255400	Enhancers	NHEK	skin
21	chr3:196254600-196255400	Enhancers	Osteobl	bone
22	chr3:196254600-196255600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:196254600-196255800	Enhancers	HepG2	liver
24	chr3:196254800-196255000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:196254800-196255000	Flanking Active TSS	A549	lung
26	chr3:196254800-196255200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:196254800-196255200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:196254800-196255200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr3:196254800-196255400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:196254800-196255400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:196254800-196255400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:196254800-196255400	Enhancers	Esophagus	oesophagus

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