Variant report

Variant	rs785499
Chromosome Location	chr1:46592420-46592421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46588282..46592472-chr1:46595758..46599785,7	MCF-7	breast:
2	chr1:46589702..46592691-chr1:46612136..46613737,2	K562	blood:
3	chr1:45972145..45974948-chr1:46590172..46592785,2	K562	blood:
4	chr1:46583710..46585229-chr1:46591036..46593047,2	K562	blood:
5	chr1:46584034..46587935-chr1:46589301..46592491,4	MCF-7	breast:
6	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
7	chr1:46580107..46581871-chr1:46591926..46594384,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117472	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1085240	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211257	0.92[ASN][1000 genomes]
rs12090501	0.88[ASN][1000 genomes]
rs1416706	0.80[ASN][1000 genomes]
rs1473840	0.81[ASN][1000 genomes]
rs1588663	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1612419	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1613296	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1622208	0.81[EUR][1000 genomes]
rs1707302	0.82[ASN][1000 genomes]
rs1707303	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1707317	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707322	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707337	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707338	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707339	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1768800	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1768801	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1768802	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1768807	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1768815	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1768817	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1768818	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297883	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2458400	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2669156	0.80[EUR][1000 genomes]
rs4660341	0.92[ASN][1000 genomes]
rs7538978	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785463	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785465	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785466	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785467	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785468	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785469	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785470	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785483	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs785484	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785486	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785490	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785493	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785496	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785497	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785498	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs785500	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785501	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785504	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs785506	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs785507	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs785508	0.81[EUR][1000 genomes]
rs785509	0.81[EUR][1000 genomes]
rs785510	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785512	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785513	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs785516	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs785517	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785518	0.87[ASN][1000 genomes]
rs785519	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs796773	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs809774	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs814168	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9429095	0.80[ASN][1000 genomes]
rs9429186	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs785499	GPBP1L1	cis	Muscle Skeletal	GTEx
rs785499	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs785499	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46540400-46595200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:46541200-46595800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:46562400-46595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:46565600-46593200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:46566800-46594000	Weak transcription	Thymus	Thymus
6	chr1:46567800-46595200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:46574000-46595200	Weak transcription	HSMM	muscle
8	chr1:46576000-46594200	Weak transcription	HMEC	breast
9	chr1:46576800-46593200	Weak transcription	Hela-S3	cervix
10	chr1:46577200-46593800	Weak transcription	Right Ventricle	heart
11	chr1:46579800-46594400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:46580400-46593400	Weak transcription	Right Atrium	heart
13	chr1:46581000-46593800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:46581800-46593400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:46581800-46595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:46582200-46593800	Weak transcription	Left Ventricle	heart
17	chr1:46584600-46595200	Weak transcription	Fetal Lung	lung
18	chr1:46585200-46593600	Weak transcription	Fetal Heart	heart
19	chr1:46588800-46593200	Weak transcription	Psoas Muscle	Psoas
20	chr1:46589400-46593400	Weak transcription	Dnd41	blood
21	chr1:46589800-46594000	Weak transcription	Adipose Nuclei	Adipose
22	chr1:46590000-46593200	Weak transcription	GM12878-XiMat	blood
23	chr1:46591400-46593200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:46592000-46592800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:46592200-46592800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:46592200-46593200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:46592200-46595200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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