Variant report

Variant	rs2650805
Chromosome Location	chr19:21687939-21687940
allele	A/C
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	RFX5	chr19:21687564-21689643	IMR90	lung:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
2	EP300	chr19:21687814-21689146	SK-N-SH	brain:	n/a	chr19:21688226-21688236
3	MAX	chr19:21687885-21689373	NB4	blood:	n/a	n/a
4	RFX5	chr19:21687624-21688952	H1-hESC	embryonic stem cell:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
5	RFX5	chr19:21687129-21689681	SK-N-SH	brain:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
6	RFX5	chr19:21687630-21689028	K562	blood:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
7	REST	chr19:21687844-21689521	H1-neurons	neurons:	n/a	n/a
8	MXI1	chr19:21687519-21689374	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ZNF429	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10420016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854050	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10854051	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11085462	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11085465	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11085468	0.81[EUR][1000 genomes]
rs1114305	0.93[CHB][hapmap]
rs11668606	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11671579	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12974758	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13346641	0.81[CEU][hapmap]
rs1879234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1967182	0.85[CEU][hapmap]
rs2086319	0.86[CHB][hapmap]
rs2173727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359144	0.85[CEU][hapmap]
rs2359155	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562398	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2562402	0.93[CHB][hapmap];0.89[CHD][hapmap]
rs2562408	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2562417	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562428	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2562435	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs2562456	0.95[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562466	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562468	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562471	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562474	0.81[AMR][1000 genomes]
rs2562487	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2562507	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2562508	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2650773	0.82[ASN][1000 genomes]
rs2650784	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650792	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650793	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650798	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2650801	0.81[ASN][1000 genomes]
rs2650804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650814	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2650819	0.82[ASN][1000 genomes]
rs2650825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650844	0.85[CEU][hapmap]
rs2681370	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681377	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2681388	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681392	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681395	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914626	0.93[CHB][hapmap]
rs2914645	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2914646	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2928218	0.90[CHB][hapmap]
rs2937174	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2946790	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968045	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2968046	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs2968076	0.80[ASN][1000 genomes]
rs2968078	0.82[ASN][1000 genomes]
rs2968082	0.93[CHB][hapmap]
rs35008138	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35099594	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4321312	1.00[CEU][hapmap]
rs4359573	1.00[CEU][hapmap]
rs4638726	0.85[CEU][hapmap]
rs4809145	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs499445	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs501563	0.92[CHB][hapmap]
rs55771551	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58001930	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110163	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs627522	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs6511250	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511254	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511258	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252254	0.82[JPT][hapmap]
rs7252585	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259708	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260065	0.95[CEU][hapmap]
rs8106025	0.82[ASN][1000 genomes]
rs8110814	0.82[JPT][hapmap]
rs924485	0.81[JPT][hapmap]
rs9304986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv543941	chr19:21676223-21693215	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2650805	ZNF738	cis	cerebellum	SCAN
rs2650805	ZNF826P	cis	parietal	SCAN
rs2650805	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2650805	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2650805	ZNF43	cis	parietal	SCAN
rs2650805	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2650805	ZNF708	cis	lung	GTEx
rs2650805	ZNF708	cis	Muscle Skeletal	GTEx
rs2650805	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2650805	ZNF493	cis	cerebellum	SCAN
rs2650805	CTD-2561J22.5	cis	Thyroid	GTEx
rs2650805	ZNF708	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21676000-21688000	Weak transcription	Fetal Stomach	stomach
2	chr19:21678000-21688000	Weak transcription	Thymus	Thymus
3	chr19:21679200-21688200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:21680000-21688200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21680200-21688200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:21681200-21688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:21681400-21688200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:21681600-21688200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:21681800-21688000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:21681800-21688000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:21681800-21688200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:21681800-21688400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:21683800-21688000	Weak transcription	Fetal Intestine Large	intestine
14	chr19:21687200-21688200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:21687200-21688200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr19:21687200-21688200	Enhancers	Primary T cells from cord blood	blood
17	chr19:21687200-21688200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:21687400-21688000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:21687400-21688000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:21687400-21688000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:21687400-21688000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr19:21687400-21688000	Enhancers	Dnd41	blood
23	chr19:21687400-21688200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:21687400-21688200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:21687600-21688000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:21687600-21688000	Enhancers	Brain Anterior Caudate	brain
27	chr19:21687600-21688000	Enhancers	Brain Cingulate Gyrus	brain
28	chr19:21687600-21688000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr19:21687600-21688000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr19:21687600-21688000	Enhancers	K562	blood
31	chr19:21687600-21688000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr19:21687600-21688200	Enhancers	Primary B cells from peripheral blood	blood
33	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr19:21687600-21688200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:21687600-21688200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:21687600-21688200	Enhancers	Liver	Liver
39	chr19:21687600-21688200	Enhancers	Duodenum Mucosa	Duodenum
40	chr19:21687600-21688200	Enhancers	Fetal Lung	lung
41	chr19:21687600-21689400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:21687600-21689600	Active TSS	Brain Germinal Matrix	brain
43	chr19:21687800-21688000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:21687800-21688000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:21687800-21688000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr19:21687800-21688000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr19:21687800-21688000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:21687800-21688000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:21687800-21688000	Enhancers	Adipose Nuclei	Adipose
50	chr19:21687800-21688000	Enhancers	Duodenum Smooth Muscle	Duodenum

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