Variant report

Variant	rs2038823
Chromosome Location	chr13:96951433-96951434
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	chr13:96951281..96952208-chr13:97448274..97448845,2	MCF-7	breast:
2	chr13:96946178..96948064-chr13:96950276..96952772,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10492589	0.91[ASN][1000 genomes]
rs11616238	0.91[ASN][1000 genomes]
rs11616565	1.00[ASN][1000 genomes]
rs11616566	0.88[ASN][1000 genomes]
rs11616575	0.91[ASN][1000 genomes]
rs11617040	1.00[ASN][1000 genomes]
rs11617420	0.94[ASN][1000 genomes]
rs11617487	0.94[ASN][1000 genomes]
rs11617543	0.91[ASN][1000 genomes]
rs11618119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618287	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11618312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618831	0.86[EUR][1000 genomes]
rs11619328	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11619375	0.91[ASN][1000 genomes]
rs11619872	0.94[ASN][1000 genomes]
rs11619967	0.91[ASN][1000 genomes]
rs11620111	1.00[ASN][1000 genomes]
rs12323049	0.94[ASN][1000 genomes]
rs1536576	0.91[ASN][1000 genomes]
rs16951460	1.00[ASN][1000 genomes]
rs16951620	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16951625	0.91[ASN][1000 genomes]
rs16951630	0.91[ASN][1000 genomes]
rs16951635	0.91[ASN][1000 genomes]
rs16951654	0.91[ASN][1000 genomes]
rs16951655	0.91[ASN][1000 genomes]
rs16951661	0.91[ASN][1000 genomes]
rs16951711	0.91[ASN][1000 genomes]
rs16951714	0.91[ASN][1000 genomes]
rs16951718	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16951722	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16951727	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16951729	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16952941	0.91[ASN][1000 genomes]
rs16953069	1.00[ASN][1000 genomes]
rs16953072	1.00[ASN][1000 genomes]
rs16953108	0.94[ASN][1000 genomes]
rs16953115	0.94[ASN][1000 genomes]
rs16953175	0.94[ASN][1000 genomes]
rs16953190	0.91[ASN][1000 genomes]
rs1925117	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925120	1.00[ASN][1000 genomes]
rs1927784	1.00[ASN][1000 genomes]
rs2104657	1.00[ASN][1000 genomes]
rs59805867	0.90[EUR][1000 genomes]
rs60769907	0.90[EUR][1000 genomes]
rs60967091	0.85[ASN][1000 genomes]
rs61966863	0.86[EUR][1000 genomes]
rs61966874	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61966876	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61966895	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61966896	0.90[EUR][1000 genomes]
rs61966898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61966902	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61966903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61966941	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61968043	0.85[EUR][1000 genomes]
rs7319851	0.91[ASN][1000 genomes]
rs73550653	0.91[ASN][1000 genomes]
rs73550662	0.91[ASN][1000 genomes]
rs73550664	0.91[ASN][1000 genomes]
rs73550684	0.91[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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv530742	chr13:96917313-97627023	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Diabetic retinopathy	21310492	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2038823	DZIP1	cis	parietal	SCAN
rs2038823	GPC5	cis	parietal	SCAN
rs2038823	CLDN10	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96948200-96951600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr13:96950000-96951600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:96950200-96951600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:96950800-96955400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:96951400-96951600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr13:96951400-96955600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:96951400-96959200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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