Variant report

Variant	rs12609823
Chromosome Location	chr19:21632719-21632720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10405716	0.85[EUR][1000 genomes]
rs1055753	0.84[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11085441	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs11085447	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs11085450	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666680	0.82[ASN][1000 genomes]
rs11667259	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667770	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11668682	0.87[ASN][1000 genomes]
rs11668691	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11669043	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669130	0.88[ASN][1000 genomes]
rs11671265	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610154	0.82[ASN][1000 genomes]
rs12975081	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12979646	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12981564	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12981735	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs12982282	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12983787	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1401926	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs17680671	0.89[CEU][hapmap]
rs1781873	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs1813234	0.81[JPT][hapmap]
rs2012013	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2088762	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2133819	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133822	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2170024	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs2358984	0.84[CHB][hapmap]
rs2650774	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28498118	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28898308	0.81[ASN][1000 genomes]
rs2914638	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs2914648	0.81[EUR][1000 genomes]
rs2914649	0.81[EUR][1000 genomes]
rs2937158	0.81[EUR][1000 genomes]
rs2937159	0.81[EUR][1000 genomes]
rs2968084	0.81[EUR][1000 genomes]
rs34152818	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35773446	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35994743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3973190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306654	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4315457	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4462731	0.81[ASN][1000 genomes]
rs4621113	0.86[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56346453	0.89[ASN][1000 genomes]
rs6511237	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6511238	0.84[EUR][1000 genomes]
rs6511239	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6511242	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6511245	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511246	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245729	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246883	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247060	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247411	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7248601	0.84[JPT][hapmap]
rs7248989	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249412	0.86[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7249636	0.81[JPT][hapmap]
rs7251620	0.83[ASN][1000 genomes]
rs7252254	0.94[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7252261	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7253249	0.94[CHB][hapmap]
rs7253886	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254059	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7254436	0.85[CEU][hapmap]
rs7254762	0.85[CEU][hapmap]
rs7257186	0.81[ASN][1000 genomes]
rs7257857	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7259311	0.86[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73017722	0.81[ASN][1000 genomes]
rs7508671	0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs8099940	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs8101089	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs8101900	0.81[ASN][1000 genomes]
rs8103325	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs8103459	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs8106840	0.81[ASN][1000 genomes]
rs8107999	0.88[CEU][hapmap]
rs8109940	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8110814	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs8110967	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs8111549	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951162	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973240	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	nsv138282	chr19:21625797-21634841	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs12609823	ZNF429	cis	Whole Blood	GTEx
rs12609823	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs12609823	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12609823	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12609823	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12609823	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs12609823	LINC00664	cis	Adipose Subcutaneous	GTEx
rs12609823	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs12609823	CTD-2561J22.5	cis	Thyroid	GTEx
rs12609823	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs12609823	ZNF493	cis	Lymphoblastoid	GTEx
rs12609823	RP11-678G14.2	cis	lung	GTEx
rs12609823	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs12609823	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs12609823	RP11-678G14.2	cis	Thyroid	GTEx
rs12609823	RP11-678G14.3	cis	lung	GTEx
rs12609823	CTD-2561J22.5	cis	lung	GTEx
rs12609823	RP11-678G14.2	cis	Artery Tibial	GTEx
rs12609823	LOC115648	cis	uninvolved skin	skin_eQTL
rs12609823	ZNF429	cis	Muscle Skeletal	GTEx
rs12609823	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12609823	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12609823	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12609823	ZNF493	cis	Heart Left Ventricle	GTEx
rs12609823	RP11-678G14.2	cis	Whole Blood	GTEx
rs12609823	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12609823	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12609823	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12609823	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs12609823	CTD-2561J22.5	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21624600-21636400	Weak transcription	Fetal Kidney	kidney
2	chr19:21629800-21641400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
3	chr19:21630000-21633000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:21630000-21642000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr19:21630200-21634600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:21630200-21643800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:21630400-21635400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:21630400-21643800	ZNF genes & repeats	Dnd41	blood
9	chr19:21630800-21635000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:21631000-21634600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:21631000-21638400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:21631400-21635200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:21631400-21635400	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:21631600-21634600	ZNF genes & repeats	Fetal Stomach	stomach
15	chr19:21631800-21638200	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr19:21632000-21637200	Weak transcription	Primary T cells from cord blood	blood
17	chr19:21632200-21633400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr19:21632200-21633800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:21632200-21634600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:21632200-21637000	Weak transcription	Fetal Lung	lung
21	chr19:21632200-21638000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:21632200-21638000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:21632400-21633200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:21632400-21633400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:21632400-21635800	Weak transcription	Thymus	Thymus
26	chr19:21632400-21637000	Weak transcription	Ovary	ovary
27	chr19:21632600-21633200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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