Variant report

Variant	rs2650801
Chromosome Location	chr19:21635355-21635356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1055753	0.83[JPT][hapmap]
rs11085441	0.80[JPT][hapmap]
rs11085447	0.83[JPT][hapmap]
rs1114305	1.00[CHB][hapmap]
rs12974758	0.81[ASN][1000 genomes]
rs12975081	0.83[JPT][hapmap]
rs12981564	0.83[JPT][hapmap]
rs12981735	0.81[JPT][hapmap]
rs12982282	0.83[JPT][hapmap]
rs1781867	0.86[CEU][hapmap]
rs1781872	0.87[CEU][hapmap]
rs1781873	0.83[JPT][hapmap]
rs2012013	0.83[JPT][hapmap]
rs2086319	0.90[CHB][hapmap]
rs2088762	0.83[JPT][hapmap]
rs2170024	0.83[JPT][hapmap]
rs2562402	1.00[CHB][hapmap]
rs2562428	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2562435	0.90[CHB][hapmap]
rs2562456	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2562474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562487	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650764	0.82[ASN][1000 genomes]
rs2650773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2650784	0.82[ASN][1000 genomes]
rs2650793	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2650798	0.90[CHB][hapmap]
rs2650805	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2650814	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2650819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914626	1.00[CHB][hapmap]
rs2914638	0.83[JPT][hapmap]
rs2914645	0.87[CHB][hapmap]
rs2914646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2928211	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2928218	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs2937174	0.90[CHB][hapmap]
rs2968022	0.90[CHB][hapmap]
rs2968045	0.90[CHB][hapmap]
rs2968046	1.00[CHB][hapmap]
rs2968072	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2968078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2968082	1.00[CHB][hapmap]
rs4315457	0.83[JPT][hapmap]
rs4321312	0.86[CEU][hapmap]
rs4359573	0.86[CEU][hapmap]
rs472472	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4809145	0.90[CHB][hapmap]
rs489845	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs499445	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs501563	0.90[CHB][hapmap]
rs516519	0.85[EUR][1000 genomes]
rs541639	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs547516	0.90[CHB][hapmap]
rs56072098	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs598959	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs600186	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs627522	0.86[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs6511239	0.82[JPT][hapmap]
rs6511250	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6511253	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6511254	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7247411	0.83[JPT][hapmap]
rs7249412	0.83[JPT][hapmap]
rs7252261	0.83[JPT][hapmap]
rs7252585	0.82[ASN][1000 genomes]
rs7257857	0.83[JPT][hapmap]
rs7259311	0.83[JPT][hapmap]
rs7508671	0.82[JPT][hapmap]
rs8099940	0.83[JPT][hapmap]
rs8103325	0.83[JPT][hapmap]
rs8103459	0.82[JPT][hapmap]
rs8106025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110967	0.83[JPT][hapmap]
rs8112775	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs924487	0.89[JPT][hapmap]
rs9304987	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3506838	chr19:21634362-21639360	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv3506836	chr19:21635212-21639260	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2650801	CTD-2561J22.5	cis	Thyroid	GTEx
rs2650801	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2650801	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2650801	ZNF708	cis	Muscle Skeletal	GTEx
rs2650801	ZNF708	cis	lung	GTEx
rs2650801	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2650801	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:35 , 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	chr19:21630000-21642000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr19:21630200-21643800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:21630400-21635400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:21630400-21643800	ZNF genes & repeats	Dnd41	blood
7	chr19:21631000-21638400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:21631400-21635400	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:21631800-21638200	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr19:21632000-21637200	Weak transcription	Primary T cells from cord blood	blood
11	chr19:21632200-21637000	Weak transcription	Fetal Lung	lung
12	chr19:21632200-21638000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:21632200-21638000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:21632400-21635800	Weak transcription	Thymus	Thymus
15	chr19:21632400-21637000	Weak transcription	Ovary	ovary
16	chr19:21633600-21637000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:21633800-21641400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:21633800-21641400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:21634400-21636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:21634600-21635400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:21634600-21635600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:21634600-21635600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:21634600-21635800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:21634600-21635800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:21634600-21636400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:21634600-21636400	Weak transcription	Fetal Stomach	stomach
27	chr19:21634600-21636600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:21634600-21637400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:21634600-21641600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:21634800-21635600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:21634800-21636400	Weak transcription	Brain Germinal Matrix	brain
32	chr19:21634800-21637400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:21635000-21635600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:21635200-21635800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:21635200-21637200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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