Variant report

Variant	rs2928211
Chromosome Location	chr19:21541297-21541298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:21541166-21542571	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr19:21541215-21542511	SK-N-SH	brain:	n/a	chr19:21541703-21541712
3	REST	chr19:21541197-21542532	H1-neurons	neurons:	n/a	chr19:21541726-21541735
4	NFYB	chr19:21541252-21542135	GM12878	blood:	n/a	chr19:21541729-21541742 chr19:21541700-21541714 chr19:21541726-21541741 chr19:21541697-21541712 chr19:21541700-21541715 chr19:21541702-21541712 chr19:21541700-21541715 chr19:21541700-21541713

Variant related genes	Relation type
ZNF738	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11666540	0.81[EUR][1000 genomes]
rs11667361	0.81[EUR][1000 genomes]
rs11670815	0.81[EUR][1000 genomes]
rs1875256	0.89[ASN][1000 genomes]
rs2061916	0.81[EUR][1000 genomes]
rs2086319	0.90[ASN][1000 genomes]
rs2434996	0.86[ASN][1000 genomes]
rs2562428	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562438	0.89[ASN][1000 genomes]
rs2562474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562487	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2650773	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2650797	0.88[ASN][1000 genomes]
rs2650798	0.88[ASN][1000 genomes]
rs2650801	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2650814	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2650819	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2650842	0.90[ASN][1000 genomes]
rs2650851	0.88[ASN][1000 genomes]
rs2914635	0.82[ASN][1000 genomes]
rs2914645	0.90[ASN][1000 genomes]
rs2914646	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2928188	0.90[ASN][1000 genomes]
rs2928209	0.93[ASN][1000 genomes]
rs2928216	0.87[ASN][1000 genomes]
rs2928218	0.90[ASN][1000 genomes]
rs2937157	0.90[ASN][1000 genomes]
rs2937174	0.88[ASN][1000 genomes]
rs2968022	0.92[ASN][1000 genomes]
rs2968023	0.90[ASN][1000 genomes]
rs2968024	0.89[ASN][1000 genomes]
rs2968040	0.88[ASN][1000 genomes]
rs2968041	0.88[ASN][1000 genomes]
rs2968045	0.88[ASN][1000 genomes]
rs2968076	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968078	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968086	0.93[ASN][1000 genomes]
rs4321312	0.81[EUR][1000 genomes]
rs4359573	0.81[EUR][1000 genomes]
rs4544364	0.81[EUR][1000 genomes]
rs475162	0.90[ASN][1000 genomes]
rs489613	0.83[ASN][1000 genomes]
rs492271	0.84[ASN][1000 genomes]
rs499445	0.84[ASN][1000 genomes]
rs501563	0.84[ASN][1000 genomes]
rs516519	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs527060	0.84[ASN][1000 genomes]
rs547516	0.83[ASN][1000 genomes]
rs555596	0.84[ASN][1000 genomes]
rs609806	0.88[ASN][1000 genomes]
rs612877	0.88[ASN][1000 genomes]
rs62107539	0.81[EUR][1000 genomes]
rs62107540	0.81[EUR][1000 genomes]
rs62107541	0.81[EUR][1000 genomes]
rs62109225	0.81[EUR][1000 genomes]
rs62109229	0.81[EUR][1000 genomes]
rs627522	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631436	0.84[ASN][1000 genomes]
rs651454	0.84[ASN][1000 genomes]
rs7258473	0.81[EUR][1000 genomes]
rs7258562	0.81[EUR][1000 genomes]
rs8106025	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs924485	0.90[ASN][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	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2928211	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2928211	ZNF708	cis	Muscle Skeletal	GTEx
rs2928211	ZNF708	cis	lung	GTEx
rs2928211	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2928211	CTD-2561J22.5	cis	Thyroid	GTEx
rs2928211	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21536200-21541400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:21536200-21541400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:21541000-21541400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:21541200-21541400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr19:21541200-21541400	Enhancers	Primary B cells from cord blood	blood
6	chr19:21541200-21541400	Enhancers	Dnd41	blood
7	chr19:21541200-21541400	Enhancers	Osteobl	bone
8	chr19:21541200-21541600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:21541200-21541600	Enhancers	Fetal Stomach	stomach
10	chr19:21541200-21543000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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