Variant report

Variant	rs7246883
Chromosome Location	chr19:21646167-21646168
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11085450	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666680	0.81[ASN][1000 genomes]
rs11667259	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668682	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11669043	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11669130	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11671265	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12609823	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610154	0.81[ASN][1000 genomes]
rs2133819	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2133822	0.81[ASN][1000 genomes]
rs2650774	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28498118	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34152818	0.81[ASN][1000 genomes]
rs35994743	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3973190	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4306654	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4621113	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56346453	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7245729	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247060	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248989	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7251620	0.81[ASN][1000 genomes]
rs7252254	0.81[ASN][1000 genomes]
rs7253886	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8101089	0.81[ASN][1000 genomes]
rs8111549	0.86[ASN][1000 genomes]
rs924487	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951162	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9973240	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[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	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs7246883	CTD-2561J22.5	cis	lung	GTEx
rs7246883	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs7246883	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs7246883	RP11-678G14.2	cis	Artery Tibial	GTEx
rs7246883	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs7246883	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs7246883	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs7246883	ZNF429	cis	Whole Blood	GTEx
rs7246883	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7246883	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7246883	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7246883	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7246883	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs7246883	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs7246883	RP11-678G14.2	cis	lung	GTEx
rs7246883	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7246883	ZNF100	cis	Muscle Skeletal	GTEx
rs7246883	ZNF429	cis	Muscle Skeletal	GTEx
rs7246883	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7246883	CTD-2561J22.5	cis	Thyroid	GTEx
rs7246883	RP11-678G14.2	cis	Thyroid	GTEx
rs7246883	LINC00664	cis	Adipose Subcutaneous	GTEx
rs7246883	RP11-678G14.3	cis	Whole Blood	GTEx
rs7246883	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs7246883	RP11-678G14.2	cis	Whole Blood	GTEx
rs7246883	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7246883	RP11-678G14.3	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21636800-21646200	Weak transcription	Fetal Heart	heart
2	chr19:21641200-21646400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr19:21642600-21646800	Active TSS	K562	blood
4	chr19:21644200-21646200	Weak transcription	Right Atrium	heart
5	chr19:21644600-21646400	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr19:21645000-21647000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:21645000-21647000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:21645200-21646600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr19:21645200-21647000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:21645200-21647000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:21645200-21647000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:21645200-21647200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:21645400-21646800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:21645400-21647000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:21645400-21647000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:21645400-21647200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:21645400-21647200	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:21645600-21646800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:21645600-21646800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:21645600-21646800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:21645600-21646800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:21645600-21646800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:21645600-21647000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:21645600-21647000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr19:21645600-21647000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:21645600-21647000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr19:21645600-21647000	Active TSS	Primary hematopoietic stem cells	blood
28	chr19:21645800-21646200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:21645800-21646200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr19:21645800-21646400	Active TSS	Placenta	Placenta
31	chr19:21645800-21646800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:21645800-21646800	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr19:21645800-21646800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:21645800-21647000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:21645800-21647000	Active TSS	Brain Germinal Matrix	brain
36	chr19:21645800-21647000	Active TSS	Fetal Kidney	kidney
37	chr19:21645800-21647000	Active TSS	Ovary	ovary
38	chr19:21645800-21647000	ZNF genes & repeats	Thymus	Thymus
39	chr19:21646000-21646200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr19:21646000-21646200	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr19:21646000-21646200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr19:21646000-21646200	Enhancers	Primary B cells from peripheral blood	blood
43	chr19:21646000-21646200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:21646000-21646200	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr19:21646000-21646200	ZNF genes & repeats	Fetal Brain Female	brain
46	chr19:21646000-21646200	Active TSS	Fetal Stomach	stomach
47	chr19:21646000-21646400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:21646000-21646600	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr19:21646000-21646800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:21646000-21646800	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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