Variant report

Variant	rs564487
Chromosome Location	chr5:177977679-177977680
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1677272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694802	0.92[EUR][1000 genomes]
rs504596	0.86[CHD][hapmap]
rs566243	0.93[EUR][1000 genomes]
rs626470	0.87[EUR][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv883215	chr5:177961860-177980792	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs564487	C5orf45	cis	cerebellum	SCAN
rs564487	IL20	trans	parietal	SCAN
rs564487	C17orf28	trans	parietal	SCAN
rs564487	NSD1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177968600-177979400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:177974400-177978400	Weak transcription	Fetal Stomach	stomach
3	chr5:177974400-177978600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:177974400-177979200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:177974400-177986200	Weak transcription	Right Atrium	heart
6	chr5:177974600-177978600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:177974600-177982400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:177975000-177982000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:177975400-177978400	Weak transcription	Fetal Heart	heart
10	chr5:177975400-177978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:177975400-177982400	Weak transcription	Right Ventricle	heart
12	chr5:177975600-177978600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:177975600-177980200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:177975600-177980200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:177975800-177980600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:177977200-177978000	Enhancers	Dnd41	blood

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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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