Variant report

Variant	rs17572822
Chromosome Location	chr4:27123561-27123562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:27123166..27125780-chr4:27126657..27128387,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16878849	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16878852	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16878854	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56077414	1.00[EUR][1000 genomes]
rs56105534	0.97[EUR][1000 genomes]
rs56159027	0.97[EUR][1000 genomes]
rs58071741	0.90[EUR][1000 genomes]
rs73251795	0.93[EUR][1000 genomes]
rs73251799	0.82[EUR][1000 genomes]
rs73251800	0.82[EUR][1000 genomes]
rs73251801	0.82[EUR][1000 genomes]
rs73251802	1.00[EUR][1000 genomes]
rs73253660	1.00[EUR][1000 genomes]
rs73253664	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73253667	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73253668	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73253670	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7685249	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002082	chr4:27078850-27377252	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv997608	chr4:27085524-27371848	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv999134	chr4:27115301-27270500	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17572822	SCGN	trans	brain	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27117400-27123600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:27122600-27125600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:27122600-27125800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:27122600-27126600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:27122800-27124400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:27122800-27124400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:27122800-27124600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:27122800-27124600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:27122800-27125600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:27122800-27126800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:27122800-27126800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr4:27122800-27127200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:27123000-27123800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:27123000-27124200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:27123000-27124600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:27123000-27126000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:27123000-27126400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr4:27123000-27127000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:27123200-27124400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr4:27123200-27125000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:27123400-27123600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:27123400-27123800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:27123400-27124000	Enhancers	Brain Inferior Temporal Lobe	brain

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