Variant report

Variant	rs12975789
Chromosome Location	chr19:21228507-21228508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10164375	0.83[ASN][1000 genomes]
rs10401931	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10405180	0.82[ASN][1000 genomes]
rs10405218	0.82[ASN][1000 genomes]
rs10406661	0.83[ASN][1000 genomes]
rs10409844	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10409877	0.82[ASN][1000 genomes]
rs10410901	0.82[ASN][1000 genomes]
rs10411038	0.82[ASN][1000 genomes]
rs10412267	0.85[ASN][1000 genomes]
rs10412688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10413175	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10413692	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10413983	0.85[ASN][1000 genomes]
rs10414134	0.85[ASN][1000 genomes]
rs10417165	1.00[ASN][1000 genomes]
rs10418706	0.92[ASN][1000 genomes]
rs10421819	0.86[ASN][1000 genomes]
rs10422193	0.95[ASN][1000 genomes]
rs10423541	0.80[ASN][1000 genomes]
rs10424283	0.85[ASN][1000 genomes]
rs10425969	0.88[ASN][1000 genomes]
rs11085424	1.00[ASN][1000 genomes]
rs11085431	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11666640	0.88[ASN][1000 genomes]
rs11666869	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668795	0.81[ASN][1000 genomes]
rs11669248	0.95[EUR][1000 genomes]
rs11670162	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11671894	0.97[ASN][1000 genomes]
rs11672142	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12104220	0.85[ASN][1000 genomes]
rs12104387	0.94[ASN][1000 genomes]
rs12608706	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12608931	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609005	0.88[ASN][1000 genomes]
rs12609167	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12609427	0.97[EUR][1000 genomes]
rs12609510	0.97[ASN][1000 genomes]
rs12609831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973640	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12974016	0.82[ASN][1000 genomes]
rs12976796	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981855	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1609441	0.85[ASN][1000 genomes]
rs1968523	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971815	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2013048	0.85[ASN][1000 genomes]
rs2081050	0.98[ASN][1000 genomes]
rs2081052	0.90[ASN][1000 genomes]
rs2081054	0.94[ASN][1000 genomes]
rs2081055	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2081056	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2081057	0.94[ASN][1000 genomes]
rs2098681	0.98[ASN][1000 genomes]
rs2099648	0.92[ASN][1000 genomes]
rs2112803	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164988	0.89[ASN][1000 genomes]
rs2164989	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2358795	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884548	0.94[ASN][1000 genomes]
rs2884554	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35137761	0.82[ASN][1000 genomes]
rs4255903	0.94[ASN][1000 genomes]
rs4292035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4365405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4488591	0.85[ASN][1000 genomes]
rs4808273	0.83[ASN][1000 genomes]
rs4808275	0.82[ASN][1000 genomes]
rs4808276	0.81[EUR][1000 genomes]
rs4809119	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62122564	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62122565	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511175	0.84[ASN][1000 genomes]
rs6511179	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511181	0.98[ASN][1000 genomes]
rs6511183	0.88[ASN][1000 genomes]
rs6511184	0.88[ASN][1000 genomes]
rs6511186	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511187	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6511188	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511191	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511192	0.82[ASN][1000 genomes]
rs6511194	0.82[ASN][1000 genomes]
rs6511195	0.82[ASN][1000 genomes]
rs6511196	0.82[ASN][1000 genomes]
rs7246723	0.85[ASN][1000 genomes]
rs7247413	1.00[ASN][1000 genomes]
rs7247553	0.92[ASN][1000 genomes]
rs7248087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248410	0.82[ASN][1000 genomes]
rs7249283	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7249736	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7250169	0.85[ASN][1000 genomes]
rs7250274	0.90[AFR][1000 genomes]
rs7252277	1.00[ASN][1000 genomes]
rs7253530	1.00[ASN][1000 genomes]
rs7254047	0.85[ASN][1000 genomes]
rs7254053	0.83[ASN][1000 genomes]
rs7254722	0.97[ASN][1000 genomes]
rs7254768	0.92[ASN][1000 genomes]
rs7254982	0.83[ASN][1000 genomes]
rs7257481	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258195	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258409	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258477	0.94[ASN][1000 genomes]
rs7258831	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259653	0.94[ASN][1000 genomes]
rs7260268	0.85[ASN][1000 genomes]
rs7260600	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7343175	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8100289	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8100599	0.85[ASN][1000 genomes]
rs8101222	0.82[ASN][1000 genomes]
rs8101412	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8101461	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8102966	0.94[ASN][1000 genomes]
rs8103696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103825	0.82[ASN][1000 genomes]
rs8106801	0.85[ASN][1000 genomes]
rs8107638	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8107982	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8109549	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8109577	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8111827	0.82[ASN][1000 genomes]
rs8112054	0.88[ASN][1000 genomes]
rs8112216	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8112500	0.82[ASN][1000 genomes]
rs8113541	0.87[AFR][1000 genomes]
rs8182465	0.82[ASN][1000 genomes]
rs9304980	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304982	0.82[ASN][1000 genomes]
rs9941463	1.00[ASN][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	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking 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	25 gene(s)	inside rSNPs	diseases
6	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv911411	chr19:21184533-21263518	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv578949	chr19:21190572-21244049	ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12975789	ZNF714	cis	Nerve Tibial	GTEx
rs12975789	ZNF714	cis	Esophagus Muscularis	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21204200-21230400	Weak transcription	Gastric	stomach
2	chr19:21204400-21229200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:21204400-21231600	Weak transcription	Colonic Mucosa	Colon
4	chr19:21204400-21264800	Weak transcription	Right Ventricle	heart
5	chr19:21204600-21239800	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:21206200-21241600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:21207200-21239400	Weak transcription	Hela-S3	cervix
8	chr19:21208600-21230000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:21209200-21235600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:21210200-21232200	Weak transcription	K562	blood
11	chr19:21211400-21235400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:21211800-21228800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:21212000-21241400	Weak transcription	Fetal Heart	heart
14	chr19:21214000-21230200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:21216000-21229800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:21217400-21230200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:21217400-21230400	Weak transcription	NHEK	skin
18	chr19:21218800-21230400	Weak transcription	NHLF	lung
19	chr19:21220400-21235200	Weak transcription	NHDF-Ad	bronchial
20	chr19:21221400-21242000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:21222400-21230800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:21222400-21242200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:21222800-21228800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:21223000-21244200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:21223200-21230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:21223400-21230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:21223400-21230200	Weak transcription	HSMMtube	muscle
28	chr19:21223400-21231400	Weak transcription	Placenta	Placenta
29	chr19:21223400-21235600	Weak transcription	NH-A	brain
30	chr19:21223600-21229800	Weak transcription	Osteobl	bone
31	chr19:21224000-21230800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:21224000-21230800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
33	chr19:21224000-21230800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr19:21224400-21230800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:21224400-21231000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr19:21224400-21232800	ZNF genes & repeats	Dnd41	blood
37	chr19:21224600-21230800	ZNF genes & repeats	Fetal Brain Female	brain
38	chr19:21224800-21230200	Weak transcription	Pancreas	Pancrea
39	chr19:21224800-21230800	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr19:21225000-21228800	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr19:21225000-21229200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:21225000-21229800	Weak transcription	Fetal Brain Male	brain
43	chr19:21225000-21230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:21225000-21230400	Weak transcription	HSMM	muscle
45	chr19:21225200-21230800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr19:21225200-21234200	Weak transcription	A549	lung
47	chr19:21225400-21228800	Weak transcription	Left Ventricle	heart
48	chr19:21225400-21230400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:21225400-21230400	Weak transcription	Esophagus	oesophagus
50	chr19:21225400-21230800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood

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