Variant report

Variant	rs1778553
Chromosome Location	chr1:247438446-247438447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247397665..247399699-chr1:247438222..247441070,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10754543	0.83[CEU][hapmap]
rs10802482	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10802483	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11579326	0.85[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs11581163	0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12081945	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12082983	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12566166	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17721193	0.84[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1778552	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211273	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2890342	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925606	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55686936	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55913685	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56245379	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56250713	0.88[EUR][1000 genomes]
rs56358050	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61838684	0.83[EUR][1000 genomes]
rs61841570	0.85[EUR][1000 genomes]
rs6426236	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426238	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6656258	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6667658	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6698384	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698803	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7544023	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7552041	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv549587	chr1:247400259-247438446	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1778553	VN1R5	cis	cerebellum	SCAN
rs1778553	EXO1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247436800-247440200	Weak transcription	Fetal Kidney	kidney
2	chr1:247436800-247457000	Weak transcription	HSMMtube	muscle
3	chr1:247437000-247439000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:247438000-247438600	Enhancers	Psoas Muscle	Psoas
5	chr1:247438000-247438600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:247438000-247438600	Enhancers	HepG2	liver
7	chr1:247438000-247438800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:247438000-247438800	Enhancers	Gastric	stomach

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