Variant report

Variant	rs28528154
Chromosome Location	chr3:98697542-98697543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:98696134-98697661	A549	lung:	n/a	chr3:98697639-98697646 chr3:98697052-98697061
2	FOXA2	chr3:98696900-98697742	A549	lung:	n/a	chr3:98697460-98697472 chr3:98697233-98697245
3	GATA3	chr3:98696060-98697575	A549	lung:	n/a	n/a

Variant related genes	Relation type
LINC00973	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10084679	0.83[AMR][1000 genomes]
rs12330381	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13094707	0.93[ASN][1000 genomes]
rs13317610	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13318536	0.93[ASN][1000 genomes]
rs13318960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320266	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13320890	0.83[AMR][1000 genomes]
rs13322253	0.85[AMR][1000 genomes]
rs13327449	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327485	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133575	0.80[ASN][1000 genomes]
rs2454687	0.80[ASN][1000 genomes]
rs2470884	0.80[ASN][1000 genomes]
rs28417568	0.85[AMR][1000 genomes]
rs28489284	0.85[AMR][1000 genomes]
rs28637457	0.93[ASN][1000 genomes]
rs28650813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821579	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28883308	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34693680	0.93[ASN][1000 genomes]
rs3796133	0.85[AMR][1000 genomes]
rs56172805	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59906228	0.85[AMR][1000 genomes]
rs6795351	0.80[ASN][1000 genomes]
rs72932691	0.85[AMR][1000 genomes]
rs72934641	0.85[AMR][1000 genomes]
rs72938540	0.88[EUR][1000 genomes]
rs7621508	0.80[ASN][1000 genomes]
rs9289696	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9810407	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9812438	0.85[AMR][1000 genomes]
rs9818215	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9819279	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819309	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9828045	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833945	0.83[AMR][1000 genomes]
rs9836437	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9836915	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9838166	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9838238	0.83[AMR][1000 genomes]
rs9838706	0.85[AMR][1000 genomes]
rs9839559	0.83[AMR][1000 genomes]
rs9842226	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848335	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848583	0.83[AMR][1000 genomes]
rs9850469	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9852537	0.83[AMR][1000 genomes]
rs9852889	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9859042	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862660	0.85[AMR][1000 genomes]
rs9864010	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872073	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872301	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879302	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883751	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs996199	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98692000-98699600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:98695000-98697800	Enhancers	HMEC	breast
3	chr3:98695400-98698800	Enhancers	Osteobl	bone
4	chr3:98696000-98699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:98696200-98697600	Enhancers	Hela-S3	cervix
6	chr3:98696200-98697600	Enhancers	NHEK	skin
7	chr3:98696400-98697600	Enhancers	HSMM	muscle
8	chr3:98696400-98697600	Enhancers	NHDF-Ad	bronchial
9	chr3:98696400-98697800	Enhancers	NHLF	lung
10	chr3:98696400-98698200	Flanking Active TSS	A549	lung
11	chr3:98696400-98699000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:98696400-98699800	Enhancers	GM12878-XiMat	blood
13	chr3:98696600-98698800	Enhancers	NH-A	brain
14	chr3:98696600-98699800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:98696800-98699000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:98696800-98700400	Enhancers	HUVEC	blood vessel
17	chr3:98697000-98697600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:98697000-98698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:98697000-98699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:98697000-98699800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:98697000-98699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:98697000-98700000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:98697200-98699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:98697200-98700000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:98697200-98705000	Weak transcription	HSMMtube	muscle
26	chr3:98697400-98698400	Weak transcription	HepG2	liver
27	chr3:98697400-98699000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:98697400-98699800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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