Variant report

Variant	rs7254762
Chromosome Location	chr19:21567022-21567023
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

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	chr19:21566734-21567333	GM12878	blood:	n/a	n/a
4	ZNF274	chr19:21565344-21567708	K562	blood:	n/a	n/a
5	ZNF274	chr19:21566608-21567947	GM08714	blood:	n/a	n/a
6	KAP1	chr19:21566663-21567592	HEK293	kidney:	n/a	n/a
7	ZNF143	chr19:21566777-21567160	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr19:21566826-21567202	K562	blood:	n/a	n/a
9	KAP1	chr19:21566832-21567178	U2OS	brain:	n/a	n/a
10	ZNF274	chr19:21565989-21567947	NT2-D1	testis:	n/a	n/a
11	SETDB1	chr19:21565882-21567756	U2OS	brain:	n/a	n/a
12	ZNF274	chr19:21566464-21567364	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000268731	TF binding region

Extended variants
information (count: 110 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1055753	0.85[CEU][hapmap]
rs11085441	0.96[CEU][hapmap]
rs11085447	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs11667770	1.00[CEU][hapmap]
rs11671832	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11673304	0.84[EUR][1000 genomes]
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]
rs12984871	0.81[EUR][1000 genomes]
rs1678822	0.85[CHB][hapmap]
rs17618715	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17618778	0.82[CHB][hapmap]
rs1762580	0.89[ASN][1000 genomes]
rs17680671	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781873	1.00[CEU][hapmap]
rs1827225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012013	1.00[CEU][hapmap]
rs2086320	0.81[AFR][1000 genomes]
rs2088762	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2102072	0.82[EUR][1000 genomes]
rs2127407	0.81[EUR][1000 genomes]
rs2127408	0.81[EUR][1000 genomes]
rs2170024	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2170025	0.81[EUR][1000 genomes]
rs2358991	0.81[EUR][1000 genomes]
rs2358992	0.81[EUR][1000 genomes]
rs2434997	0.81[EUR][1000 genomes]
rs2914636	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2914637	0.89[ASN][1000 genomes]
rs2914638	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs2914648	0.81[AMR][1000 genomes]
rs2914649	0.81[AMR][1000 genomes]
rs2928210	0.89[ASN][1000 genomes]
rs2937158	0.81[AMR][1000 genomes]
rs2937159	0.81[AMR][1000 genomes]
rs2968084	0.81[AMR][1000 genomes]
rs34875588	0.89[ASN][1000 genomes]
rs35860067	0.89[ASN][1000 genomes]
rs4315457	1.00[CEU][hapmap]
rs4621113	1.00[CEU][hapmap]
rs483383	0.89[ASN][1000 genomes]
rs488125	0.89[YRI][hapmap]
rs501647	1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs504280	0.80[YRI][hapmap]
rs509540	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs514390	0.84[ASN][1000 genomes]
rs549882	0.89[ASN][1000 genomes]
rs552039	0.89[ASN][1000 genomes]
rs566230	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs57055133	0.89[ASN][1000 genomes]
rs58121117	0.89[ASN][1000 genomes]
rs59617671	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs608002	0.89[ASN][1000 genomes]
rs62107470	0.89[ASN][1000 genomes]
rs62107538	0.89[ASN][1000 genomes]
rs62109224	0.89[ASN][1000 genomes]
rs62110379	0.89[ASN][1000 genomes]
rs62110417	0.94[AMR][1000 genomes]
rs62110418	0.95[AMR][1000 genomes]
rs629548	0.82[CHB][hapmap]
rs635730	0.82[ASN][1000 genomes]
rs6511239	1.00[CEU][hapmap]
rs669046	0.85[CHB][hapmap]
rs670813	0.89[ASN][1000 genomes]
rs685844	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs7245848	0.89[ASN][1000 genomes]
rs7246684	0.89[ASN][1000 genomes]
rs7247411	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7248601	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7248700	0.87[ASN][1000 genomes]
rs7249412	1.00[CEU][hapmap]
rs7252261	1.00[CEU][hapmap]
rs7254436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7257580	0.87[EUR][1000 genomes]
rs7257857	1.00[CEU][hapmap]
rs7259311	1.00[CEU][hapmap]
rs73025767	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7508671	1.00[CEU][hapmap]
rs8099863	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8099940	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs8103325	1.00[CEU][hapmap]
rs8103411	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103417	0.84[ASN][1000 genomes]
rs8103459	1.00[CEU][hapmap]
rs8105404	0.89[ASN][1000 genomes]
rs8105629	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs8107999	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs8110967	1.00[CEU][hapmap]
rs8111189	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8112583	0.81[EUR][1000 genomes]
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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7254762	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7254762	RP11-678G14.2	cis	lung	GTEx
rs7254762	ZNF493	cis	Thyroid	GTEx
rs7254762	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7254762	CTD-2561J22.5	cis	lung	GTEx
rs7254762	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs7254762	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7254762	CTD-2561J22.5	cis	Stomach	GTEx
rs7254762	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs7254762	RP11-678G14.2	cis	Whole Blood	GTEx
rs7254762	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7254762	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7254762	RP11-678G14.2	cis	Thyroid	GTEx
rs7254762	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7254762	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7254762	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs7254762	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs7254762	CTD-2561J22.5	cis	Thyroid	GTEx
rs7254762	RP11-678G14.3	cis	lung	GTEx
rs7254762	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links