Variant report

Variant	rs7778357
Chromosome Location	chr7:48154273-48154274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10225490	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10278827	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1033738	chr7:48143988-48349357	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7778357	YKT6	cis	parietal	SCAN
rs7778357	PKD1L1	cis	cerebellum	SCAN
rs7778357	UPP1	cis	cerebellum	SCAN
rs7778357	PKD1L1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48138800-48156200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:48143000-48156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:48148000-48155800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:48148600-48158200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:48149000-48155800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:48149400-48156200	Weak transcription	Spleen	Spleen
7	chr7:48149600-48155800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:48151400-48154400	Enhancers	NHEK	skin
9	chr7:48151800-48154600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:48151800-48154600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:48151800-48154800	Enhancers	HMEC	breast
12	chr7:48151800-48155400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:48153200-48154600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:48153600-48154600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:48153600-48154600	Enhancers	Esophagus	oesophagus
16	chr7:48153600-48154600	Enhancers	Placenta	Placenta
17	chr7:48154000-48154600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:48154200-48154400	Enhancers	Aorta	Aorta

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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