Variant report

Variant	rs35230828
Chromosome Location	chr19:21738391-21738392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1012040	0.80[AMR][1000 genomes]
rs1021722	0.86[AMR][1000 genomes]
rs10404462	0.85[AMR][1000 genomes]
rs10406824	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10406870	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10411757	0.83[AMR][1000 genomes]
rs10412139	0.86[AMR][1000 genomes]
rs10412656	0.86[AMR][1000 genomes]
rs10414373	0.85[AMR][1000 genomes]
rs10420166	0.85[AMR][1000 genomes]
rs10423403	0.86[AMR][1000 genomes]
rs11085455	0.90[AMR][1000 genomes]
rs12974019	0.82[EUR][1000 genomes]
rs12975330	0.85[AMR][1000 genomes]
rs12976011	0.86[AMR][1000 genomes]
rs1500400	0.85[AMR][1000 genomes]
rs1500401	0.86[AMR][1000 genomes]
rs1520071	0.86[AMR][1000 genomes]
rs1520072	0.85[AMR][1000 genomes]
rs1520073	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1566474	0.86[AMR][1000 genomes]
rs1566476	0.86[AMR][1000 genomes]
rs1566477	0.86[AMR][1000 genomes]
rs1607664	0.85[AMR][1000 genomes]
rs16997924	0.86[AMR][1000 genomes]
rs1879235	0.85[AMR][1000 genomes]
rs1963056	0.85[AMR][1000 genomes]
rs1984771	0.85[AMR][1000 genomes]
rs2056319	0.83[AMR][1000 genomes]
rs2062564	0.85[AMR][1000 genomes]
rs2090707	0.86[AMR][1000 genomes]
rs2133816	0.86[AMR][1000 genomes]
rs2133820	0.85[AMR][1000 genomes]
rs2133821	0.85[AMR][1000 genomes]
rs2173723	0.85[AMR][1000 genomes]
rs2173724	0.86[AMR][1000 genomes]
rs2246914	0.86[AMR][1000 genomes]
rs2262897	0.86[AMR][1000 genomes]
rs2359162	0.85[AMR][1000 genomes]
rs2454919	0.85[AMR][1000 genomes]
rs2562399	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562419	0.90[AMR][1000 genomes]
rs2562441	0.85[AMR][1000 genomes]
rs2562448	0.85[AMR][1000 genomes]
rs2562451	0.86[AMR][1000 genomes]
rs2562452	0.86[AMR][1000 genomes]
rs2562453	0.86[AMR][1000 genomes]
rs2562454	0.86[AMR][1000 genomes]
rs2562455	0.86[AMR][1000 genomes]
rs2562457	0.86[AMR][1000 genomes]
rs2562458	0.86[AMR][1000 genomes]
rs2562459	0.86[AMR][1000 genomes]
rs2562472	0.83[AMR][1000 genomes]
rs2562473	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562496	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2650757	0.85[AMR][1000 genomes]
rs2650759	0.88[AMR][1000 genomes]
rs2650760	0.86[AMR][1000 genomes]
rs2650778	0.86[AMR][1000 genomes]
rs2650779	0.86[AMR][1000 genomes]
rs2650780	0.86[AMR][1000 genomes]
rs2650781	0.86[AMR][1000 genomes]
rs2650782	0.86[AMR][1000 genomes]
rs2650783	0.86[AMR][1000 genomes]
rs2650785	0.86[AMR][1000 genomes]
rs2650786	0.86[AMR][1000 genomes]
rs2650787	0.86[AMR][1000 genomes]
rs2650788	0.83[AMR][1000 genomes]
rs2650791	0.85[AMR][1000 genomes]
rs2650794	0.86[AMR][1000 genomes]
rs2650799	0.86[AMR][1000 genomes]
rs2650806	0.85[AMR][1000 genomes]
rs2650807	0.85[AMR][1000 genomes]
rs2650808	0.86[AMR][1000 genomes]
rs2650827	0.86[AMR][1000 genomes]
rs2650829	0.85[AMR][1000 genomes]
rs2650830	0.85[AMR][1000 genomes]
rs2650834	0.86[AMR][1000 genomes]
rs2650835	0.85[AMR][1000 genomes]
rs2681365	0.86[AMR][1000 genomes]
rs2681366	0.85[AMR][1000 genomes]
rs2681368	0.86[AMR][1000 genomes]
rs2681371	0.86[AMR][1000 genomes]
rs2681372	0.86[AMR][1000 genomes]
rs2681375	0.85[AMR][1000 genomes]
rs2681380	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681382	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681383	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681384	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681390	0.86[AMR][1000 genomes]
rs2968081	0.86[AMR][1000 genomes]
rs34006898	0.90[AMR][1000 genomes]
rs34978316	0.82[AMR][1000 genomes]
rs35088652	0.90[AMR][1000 genomes]
rs35245030	0.86[AMR][1000 genomes]
rs35366148	0.83[AMR][1000 genomes]
rs35506714	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35595475	0.82[EUR][1000 genomes]
rs35991360	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4332859	0.91[AMR][1000 genomes]
rs4574048	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4611587	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56764276	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58818104	0.91[AMR][1000 genomes]
rs59654184	0.90[AMR][1000 genomes]
rs62108277	0.86[AMR][1000 genomes]
rs62108280	0.83[AMR][1000 genomes]
rs62108331	0.90[AMR][1000 genomes]
rs62108332	0.85[AMR][1000 genomes]
rs62108335	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62111480	0.82[AMR][1000 genomes]
rs6511261	0.86[AMR][1000 genomes]
rs7248097	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254872	0.90[AMR][1000 genomes]
rs7257584	0.86[AMR][1000 genomes]
rs7258523	0.86[AMR][1000 genomes]
rs7258901	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs74167858	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74167860	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7507813	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8100193	0.83[AMR][1000 genomes]
rs8100318	0.85[AMR][1000 genomes]
rs8101442	0.86[AMR][1000 genomes]
rs8102699	0.82[AMR][1000 genomes]
rs8102854	0.88[AMR][1000 genomes]
rs8103967	0.83[EUR][1000 genomes]
rs8106433	0.90[AMR][1000 genomes]
rs8111788	0.85[AMR][1000 genomes]
rs8112359	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	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
9	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35230828	ZNF429	cis	Whole Blood	GTEx
rs35230828	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs35230828	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs35230828	ZNF738	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21720400-21740800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr19:21726400-21740800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:21726600-21740800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:21735800-21741600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:21735800-21744800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:21736200-21741400	ZNF genes & repeats	Liver	Liver
7	chr19:21736400-21743000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21736800-21738400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:21737000-21738800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:21737200-21738600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:21737200-21743000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:21737200-21747200	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr19:21737400-21738400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
14	chr19:21737400-21738600	ZNF genes & repeats	Colonic Mucosa	Colon
15	chr19:21737400-21738600	ZNF genes & repeats	Lung	lung
16	chr19:21737400-21738800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr19:21737400-21738800	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr19:21737400-21738800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
19	chr19:21737400-21739400	ZNF genes & repeats	Fetal Lung	lung
20	chr19:21737400-21739400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:21737400-21739600	ZNF genes & repeats	Fetal Stomach	stomach
22	chr19:21737600-21738600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr19:21737600-21738600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:21737600-21738600	ZNF genes & repeats	Fetal Kidney	kidney
25	chr19:21737600-21738600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr19:21737600-21738800	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr19:21737600-21739000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:21737800-21738600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:21737800-21738600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:21737800-21738600	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr19:21737800-21738600	ZNF genes & repeats	Gastric	stomach
32	chr19:21737800-21738600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
33	chr19:21737800-21738600	Strong transcription	Right Ventricle	heart
34	chr19:21737800-21738800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:21737800-21738800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:21737800-21738800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:21737800-21738800	ZNF genes & repeats	Aorta	Aorta
38	chr19:21737800-21738800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:21737800-21738800	ZNF genes & repeats	Thymus	Thymus
40	chr19:21737800-21739000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:21737800-21739800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
42	chr19:21738000-21738800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
43	chr19:21738000-21739000	Strong transcription	Dnd41	blood
44	chr19:21738000-21739400	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr19:21738000-21749400	Weak transcription	Left Ventricle	heart
46	chr19:21738000-21751400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr19:21738200-21738400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr19:21738200-21738400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
49	chr19:21738200-21738600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:21738200-21738800	ZNF genes & repeats	Ovary	ovary

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