Variant report

Variant	rs28512414
Chromosome Location	chr19:38056574-38056575
allele	A/T
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	ZNF274	chr19:38053448-38059008	K562	blood:	n/a	n/a
2	ZNF274	chr19:38055336-38056709	K562	blood:	n/a	n/a
3	ZNF274	chr19:38054832-38057196	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr19:38056560-38056710	HL-60	blood:	n/a	n/a
5	KAP1	chr19:38054975-38056842	U2OS	brain:	n/a	n/a
6	TCF12	chr19:38055253-38056981	A549	lung:	n/a	n/a
7	KAP1	chr19:38054939-38057168	HEK293	kidney:	n/a	n/a
8	GATA3	chr19:38055188-38057034	A549	lung:	n/a	n/a
9	KAP1	chr19:38054457-38056841	K562	blood:	n/a	n/a
10	SETDB1	chr19:38054557-38056968	K562	blood:	n/a	n/a
11	ZNF274	chr19:38054941-38056853	GM12878	blood:	n/a	n/a
12	ZNF274	chr19:38055304-38057111	GM08714	blood:	n/a	n/a
13	ZNF274	chr19:38055277-38056818	HepG2	liver:	n/a	n/a
14	ZNF274	chr19:38055283-38056787	NT2-D1	testis:	n/a	n/a
15	SETDB1	chr19:38054440-38057341	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ZNF571-AS1	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10402671	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403173	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10404031	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10406379	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10408619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409605	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10410588	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10412510	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412786	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10417576	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10420552	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10425795	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083432	0.89[EUR][1000 genomes]
rs12459015	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12979640	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13744	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531549	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564206	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1564208	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958861	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16958863	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1975937	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1975939	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075284	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2287229	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291002	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909085	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2909088	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2909093	0.83[EUR][1000 genomes]
rs2909098	0.81[EUR][1000 genomes]
rs2909102	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909105	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909109	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2927739	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2927742	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2927746	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2927747	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972430	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972434	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972446	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972447	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972448	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2972452	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2972458	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3101746	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3101747	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3112433	0.82[ASN][1000 genomes]
rs3112434	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35863684	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829688	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803215	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803233	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803262	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803263	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803287	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56151076	0.85[ASN][1000 genomes]
rs6508736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100646	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8103647	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8110865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304568	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs954504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958305	0.86[EUR][1000 genomes]
rs968073	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9749368	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9797618	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9941475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28512414	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
2	chr19:38032600-38075200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:38041200-38079600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38041800-38059600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:38045000-38078600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:38046400-38067200	ZNF genes & repeats	Brain Substantia Nigra	brain
9	chr19:38046400-38071800	ZNF genes & repeats	Brain Hippocampus Middle	brain
10	chr19:38046600-38066800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:38047000-38058600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
13	chr19:38047400-38067000	ZNF genes & repeats	Brain Anterior Caudate	brain
14	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:38049200-38079600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:38050000-38057400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:38051400-38058800	ZNF genes & repeats	Fetal Lung	lung
18	chr19:38051400-38059600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:38051400-38059800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
20	chr19:38051400-38066800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
21	chr19:38051600-38058200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:38051600-38061600	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr19:38051600-38077600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr19:38051600-38078800	ZNF genes & repeats	Fetal Brain Female	brain
25	chr19:38052000-38057800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr19:38052000-38061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:38052000-38067000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
28	chr19:38052000-38067200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr19:38052200-38058200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr19:38052200-38061600	ZNF genes & repeats	Dnd41	blood
31	chr19:38052200-38067000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:38052200-38075200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr19:38052200-38078600	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr19:38052400-38058600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
35	chr19:38052400-38059800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
36	chr19:38052400-38061400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:38052600-38057200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:38053000-38058600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:38053200-38063200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:38053200-38064600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
41	chr19:38053200-38078200	ZNF genes & repeats	Brain Germinal Matrix	brain
42	chr19:38053200-38078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:38053400-38058800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
44	chr19:38053400-38061800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr19:38053400-38064400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr19:38053400-38078400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:38054400-38058600	ZNF genes & repeats	Fetal Heart	heart
48	chr19:38054400-38059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:38054600-38058600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:38055000-38057400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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