Variant report

Variant	rs7543460
Chromosome Location	chr1:77859881-77859882
allele	C/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	GATA3	chr1:77859667-77860320	SK-N-SH	brain:	n/a	chr1:77859968-77859980
2	PBX3	chr1:77859837-77860259	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000221664	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12567557	0.86[ASN][1000 genomes]
rs12748599	0.94[ASN][1000 genomes]
rs3844165	0.97[ASN][1000 genomes]
rs55944358	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS 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
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:77847400-77860200	Weak transcription	HSMM	muscle
5	chr1:77854000-77865200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:77854200-77860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:77854200-77863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:77854200-77864200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:77854800-77860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:77854800-77862600	Weak transcription	Aorta	Aorta
11	chr1:77855000-77860000	Weak transcription	NHLF	lung
12	chr1:77855000-77863800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:77858400-77860000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:77858400-77860000	Weak transcription	Osteobl	bone
15	chr1:77858400-77860200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:77858600-77860000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:77858600-77860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:77859000-77860400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:77859200-77861400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:77859200-77862600	Enhancers	NHDF-Ad	bronchial
21	chr1:77859400-77860600	Enhancers	Brain Substantia Nigra	brain
22	chr1:77859400-77861400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:77859400-77865600	Enhancers	Brain Anterior Caudate	brain
24	chr1:77859600-77861600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:77859600-77861600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:77859800-77865600	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:77859800-77866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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