Variant report

Variant	rs7254436
Chromosome Location	chr19:21566680-21566681
allele	C/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	ZNF274	chr19:21565995-21567348	HepG2	liver:	n/a	n/a
2	ZNF274	chr19:21565721-21567608	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF274	chr19:21565344-21567708	K562	blood:	n/a	n/a
4	ZNF274	chr19:21566608-21567947	GM08714	blood:	n/a	n/a
5	KAP1	chr19:21566663-21567592	HEK293	kidney:	n/a	n/a
6	ZNF274	chr19:21565989-21567947	NT2-D1	testis:	n/a	n/a
7	SETDB1	chr19:21565882-21567756	U2OS	brain:	n/a	n/a
8	ZNF274	chr19:21566464-21567364	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-1	chr19:21560191-21571384	NR_027130
2	lnc-ZNF708-8	chr19:21566420-21568648	ucscGeneNc_uc002nqg_2

Variant related genes	Relation type
ENSG00000268731	TF binding region
ENSG00000213976	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1055753	0.85[CEU][hapmap]
rs11085441	0.96[CEU][hapmap]
rs11085447	0.96[CEU][hapmap]
rs11667770	1.00[CEU][hapmap]
rs12975081	0.96[CEU][hapmap]
rs12975981	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12981564	1.00[CEU][hapmap]
rs12981735	1.00[CEU][hapmap]
rs12981869	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12982282	1.00[CEU][hapmap]
rs1678822	0.85[CHB][hapmap]
rs17618715	1.00[CHB][hapmap]
rs17618778	0.82[CHB][hapmap]
rs17680671	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1781873	1.00[CEU][hapmap]
rs2012013	1.00[CEU][hapmap]
rs2088762	1.00[CEU][hapmap]
rs2170024	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs2914636	1.00[CHB][hapmap]
rs2914638	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs4315457	1.00[CEU][hapmap]
rs4621113	1.00[CEU][hapmap]
rs488125	0.89[YRI][hapmap]
rs501647	1.00[CHB][hapmap];0.90[YRI][hapmap]
rs504280	0.80[YRI][hapmap]
rs509540	1.00[CHB][hapmap]
rs566230	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs629548	0.82[CHB][hapmap]
rs6511239	1.00[CEU][hapmap]
rs669046	0.85[CHB][hapmap]
rs685844	1.00[CHB][hapmap]
rs7247411	1.00[CEU][hapmap]
rs7248601	0.91[CEU][hapmap]
rs7249412	1.00[CEU][hapmap]
rs7252261	1.00[CEU][hapmap]
rs7254762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7257857	1.00[CEU][hapmap]
rs7259311	1.00[CEU][hapmap]
rs7508671	1.00[CEU][hapmap]
rs8099940	1.00[CEU][hapmap]
rs8103325	1.00[CEU][hapmap]
rs8103459	1.00[CEU][hapmap]
rs8105629	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs8107999	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs8110967	1.00[CEU][hapmap]
rs8111189	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs8113558	0.82[CHB][hapmap]
rs924487	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7254436	CTD-2561J22.5	cis	Stomach	GTEx
rs7254436	RP11-678G14.2	cis	lung	GTEx
rs7254436	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7254436	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7254436	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7254436	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7254436	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs7254436	RP11-678G14.2	cis	Thyroid	GTEx
rs7254436	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7254436	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs7254436	RP11-678G14.2	cis	Whole Blood	GTEx
rs7254436	CTD-2561J22.5	cis	lung	GTEx
rs7254436	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs7254436	RP11-678G14.3	cis	lung	GTEx
rs7254436	ZNF493	cis	Thyroid	GTEx
rs7254436	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7254436	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21543000-21566800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:21543400-21570600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:21543800-21567400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:21544200-21567400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:21544200-21567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:21547400-21567600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:21547800-21571000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:21551000-21570800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:21552000-21570800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:21555000-21566800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr19:21555800-21567000	ZNF genes & repeats	Dnd41	blood
12	chr19:21556800-21569400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr19:21558000-21566800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:21558000-21567400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr19:21558000-21567400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:21560400-21567200	ZNF genes & repeats	Fetal Lung	lung
17	chr19:21560400-21567600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr19:21560400-21568000	ZNF genes & repeats	Liver	Liver
19	chr19:21561000-21569800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr19:21561400-21566800	ZNF genes & repeats	Fetal Brain Female	brain
21	chr19:21561400-21567600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:21561800-21568000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr19:21565000-21569800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr19:21565200-21567400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:21565400-21567600	Weak transcription	Ovary	ovary
26	chr19:21565400-21567800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:21565600-21567400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
28	chr19:21565600-21570400	ZNF genes & repeats	Adipose Nuclei	Adipose
29	chr19:21565800-21566800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:21565800-21567800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:21566000-21567000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
32	chr19:21566000-21567200	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr19:21566000-21567200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
34	chr19:21566200-21567400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:21566400-21568000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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