Variant report

Variant	rs28392728
Chromosome Location	chr7:112724147-112724148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112721230..112724199-chr7:112725875..112727667,2	K562	blood:
2	chr7:112723034..112725310-chr7:112753782..112755599,2	MCF-7	breast:
3	chr7:112723161..112726364-chr7:112726656..112729737,3	K562	blood:

Variant related genes	Relation type
ENSG00000164604	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10267651	0.82[ASW][hapmap];0.82[LWK][hapmap]
rs6951139	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6972406	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7788888	1.00[AMR][1000 genomes]
rs7792704	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3355135	chr7:112616979-113134651	Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv435847	chr7:112618576-113134022	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3430638	chr7:112620663-113134403	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3442221	chr7:112620665-113134971	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv993501	chr7:112625029-113125338	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1022066	chr7:112630168-113122748	Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv539090	chr7:112630168-113122748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv889057	chr7:112652854-112734225	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
11	nsv889058	chr7:112652854-112737222	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28392728	SYCE1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112721200-112727800	Active TSS	Brain Anterior Caudate	brain
2	chr7:112721200-112728000	Active TSS	Brain Angular Gyrus	brain
3	chr7:112721400-112724200	Active TSS	Fetal Brain Male	brain
4	chr7:112722000-112724200	Active TSS	Brain Cingulate Gyrus	brain
5	chr7:112722400-112727800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:112723000-112724200	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:112723200-112724800	Flanking Active TSS	Fetal Brain Female	brain
8	chr7:112723400-112724400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:112723400-112724600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:112723400-112724600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:112723400-112724800	Enhancers	Fetal Stomach	stomach
12	chr7:112723400-112725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:112723400-112725800	Weak transcription	Pancreas	Pancrea
14	chr7:112723600-112724200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:112723600-112724200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr7:112723600-112724200	Enhancers	Brain Germinal Matrix	brain
17	chr7:112723600-112724200	Enhancers	Fetal Muscle Leg	muscle
18	chr7:112723600-112725400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:112723800-112725800	Weak transcription	Right Ventricle	heart
20	chr7:112724000-112724200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:112724000-112724400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr7:112724000-112724600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:112724000-112725600	Enhancers	K562	blood

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