Variant report

Variant	rs59417372
Chromosome Location	chr1:77861491-77861492
allele	A/C
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	chr1:77861220-77861865	SK-N-SH	brain:	n/a	chr1:77861549-77861556 chr1:77861542-77861563 chr1:77861549-77861556 chr1:77861545-77861561 chr1:77861565-77861574 chr1:77861549-77861556
2	TCF12	chr1:77860966-77861546	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000221664	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10518551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518553	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162337	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162338	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736701	0.87[ASN][1000 genomes]
rs17100530	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17379910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17380099	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349965	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647514	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647517	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647518	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647519	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647521	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2803143	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2803146	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2882289	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3104461	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112829	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342893	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402168	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703133	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415865	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7417056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:77854000-77865200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:77854200-77863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:77854200-77864200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:77854800-77862600	Weak transcription	Aorta	Aorta
7	chr1:77855000-77863800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:77859200-77862600	Enhancers	NHDF-Ad	bronchial
9	chr1:77859400-77865600	Enhancers	Brain Anterior Caudate	brain
10	chr1:77859600-77861600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:77859600-77861600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:77859800-77865600	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:77859800-77866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:77860000-77862800	Enhancers	Osteobl	bone
15	chr1:77860000-77866200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:77860000-77866600	Enhancers	Brain Hippocampus Middle	brain
17	chr1:77860200-77861600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:77860200-77861600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:77860200-77862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:77860400-77864000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:77860800-77862800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:77860800-77866000	Enhancers	Brain Angular Gyrus	brain
23	chr1:77861000-77866400	Enhancers	Brain Substantia Nigra	brain
24	chr1:77861200-77861800	Genic enhancers	HSMM	muscle
25	chr1:77861200-77862400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:77861200-77865000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:77861200-77865000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:77861400-77862200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:77861400-77862400	Weak transcription	HSMMtube	muscle
30	chr1:77861400-77863200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:77861400-77863600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:77861400-77863800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:77861400-77865600	Enhancers	Brain Inferior Temporal Lobe	brain

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