Variant report

Variant	rs12973640
Chromosome Location	chr19:21265759-21265760
allele	A/G
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	chr19:21264301-21265937	SK-N-SH	brain:	n/a	chr19:21264920-21264929 chr19:21264859-21264868 chr19:21264856-21264871
2	MXI1	chr19:21264617-21265852	IMR90	lung:	n/a	n/a
3	MXI1	chr19:21264424-21265910	SK-N-SH	brain:	n/a	n/a
4	CHD1	chr19:21264761-21265844	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr19:21264448-21265799	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:21238270..21239771-chr19:21264302..21266943,2	K562	blood:
2	chr19:21246343..21248444-chr19:21263959..21266875,2	K562	blood:
3	chr17:57969004..57971186-chr19:21264179..21266125,2	MCF-7	breast:
4	chr19:21203269..21205162-chr19:21263863..21266449,2	MCF-7	breast:

Variant related genes	Relation type
ZNF714	TF binding region
ENSG00000268598	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000118620	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000265650	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10164375	0.98[ASN][1000 genomes]
rs10401931	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403266	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10405180	0.91[ASN][1000 genomes]
rs10405218	0.97[ASN][1000 genomes]
rs10405406	0.85[ASN][1000 genomes]
rs10406661	0.98[ASN][1000 genomes]
rs10409844	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409877	0.91[ASN][1000 genomes]
rs10410901	0.97[ASN][1000 genomes]
rs10411038	0.97[ASN][1000 genomes]
rs10412267	1.00[ASN][1000 genomes]
rs10412509	0.80[ASN][1000 genomes]
rs10412688	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10413175	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413226	0.85[AFR][1000 genomes]
rs10413692	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10413983	1.00[ASN][1000 genomes]
rs10414134	1.00[ASN][1000 genomes]
rs10417165	0.85[ASN][1000 genomes]
rs10421819	0.98[ASN][1000 genomes]
rs10422193	0.81[ASN][1000 genomes]
rs10423541	0.89[ASN][1000 genomes]
rs10424283	1.00[ASN][1000 genomes]
rs10425969	0.97[ASN][1000 genomes]
rs10454116	0.84[ASN][1000 genomes]
rs11085424	0.85[ASN][1000 genomes]
rs11085431	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666640	0.97[ASN][1000 genomes]
rs11666869	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11667674	0.88[ASN][1000 genomes]
rs11668952	0.88[ASN][1000 genomes]
rs11668985	0.86[ASN][1000 genomes]
rs11669248	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11670162	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671397	0.88[ASN][1000 genomes]
rs11671894	0.82[ASN][1000 genomes]
rs11672142	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672727	0.88[ASN][1000 genomes]
rs11672747	0.88[ASN][1000 genomes]
rs11878599	0.88[ASN][1000 genomes]
rs12104220	1.00[ASN][1000 genomes]
rs12608706	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12608931	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12609005	0.97[ASN][1000 genomes]
rs12609167	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609427	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12609510	0.82[ASN][1000 genomes]
rs12609831	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12611115	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12973921	0.88[ASN][1000 genomes]
rs12974016	0.97[ASN][1000 genomes]
rs12975789	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12976796	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12981855	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1470021	0.94[ASN][1000 genomes]
rs1470022	0.94[ASN][1000 genomes]
rs1609441	1.00[ASN][1000 genomes]
rs1968523	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971815	0.88[AMR][1000 genomes]
rs2013048	1.00[ASN][1000 genomes]
rs2081050	0.83[ASN][1000 genomes]
rs2081055	0.86[EUR][1000 genomes]
rs2081056	0.86[EUR][1000 genomes]
rs2082003	0.88[ASN][1000 genomes]
rs2098681	0.83[ASN][1000 genomes]
rs2112803	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2115493	0.87[ASN][1000 genomes]
rs2115494	0.88[ASN][1000 genomes]
rs2115495	0.88[ASN][1000 genomes]
rs2164988	0.92[ASN][1000 genomes]
rs2164989	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2195453	0.88[ASN][1000 genomes]
rs2195454	0.88[ASN][1000 genomes]
rs2358792	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2358795	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2358803	0.88[ASN][1000 genomes]
rs2358804	0.88[ASN][1000 genomes]
rs2884554	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34726293	0.90[AFR][1000 genomes]
rs35137761	0.97[ASN][1000 genomes]
rs4292035	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4365405	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4488591	1.00[ASN][1000 genomes]
rs4808275	0.97[ASN][1000 genomes]
rs4808276	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4809119	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809122	0.94[ASN][1000 genomes]
rs62122564	0.86[EUR][1000 genomes]
rs62122565	0.86[EUR][1000 genomes]
rs6511179	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511181	0.83[ASN][1000 genomes]
rs6511183	0.97[ASN][1000 genomes]
rs6511184	0.97[ASN][1000 genomes]
rs6511185	0.88[ASN][1000 genomes]
rs6511186	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511187	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511188	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511190	0.86[ASN][1000 genomes]
rs6511191	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511192	0.97[ASN][1000 genomes]
rs6511194	0.97[ASN][1000 genomes]
rs6511195	0.97[ASN][1000 genomes]
rs6511196	0.91[ASN][1000 genomes]
rs6511198	0.88[ASN][1000 genomes]
rs6511199	0.88[ASN][1000 genomes]
rs6511200	0.88[ASN][1000 genomes]
rs6511201	0.88[ASN][1000 genomes]
rs7246723	1.00[ASN][1000 genomes]
rs7247413	0.85[ASN][1000 genomes]
rs7248087	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7248410	0.97[ASN][1000 genomes]
rs7249283	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249736	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250169	1.00[ASN][1000 genomes]
rs7252277	0.85[ASN][1000 genomes]
rs7253530	0.85[ASN][1000 genomes]
rs7253950	0.94[ASN][1000 genomes]
rs7254047	1.00[ASN][1000 genomes]
rs7254053	0.98[ASN][1000 genomes]
rs7254722	0.82[ASN][1000 genomes]
rs7254982	0.98[ASN][1000 genomes]
rs7257481	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258195	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258409	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258831	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7260268	1.00[ASN][1000 genomes]
rs7260600	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343175	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741674	0.94[ASN][1000 genomes]
rs741676	0.94[ASN][1000 genomes]
rs8100289	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100599	1.00[ASN][1000 genomes]
rs8101222	0.91[ASN][1000 genomes]
rs8101412	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101461	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8103696	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8103825	0.97[ASN][1000 genomes]
rs8106801	1.00[ASN][1000 genomes]
rs8106923	0.94[ASN][1000 genomes]
rs8107638	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107982	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109549	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8109577	0.82[EUR][1000 genomes]
rs8111827	0.91[ASN][1000 genomes]
rs8112054	0.97[ASN][1000 genomes]
rs8112216	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112500	0.97[ASN][1000 genomes]
rs8182465	0.97[ASN][1000 genomes]
rs9304980	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304981	0.80[ASN][1000 genomes]
rs9304982	0.91[ASN][1000 genomes]
rs9941463	0.85[ASN][1000 genomes]
rs9967619	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
8	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv911412	chr19:21233388-21297358	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12973640	ZNF714	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21247400-21289600	Weak transcription	Aorta	Aorta
2	chr19:21264600-21265800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr19:21264600-21265800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:21264600-21265800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:21264600-21266000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:21264600-21266000	Active TSS	Fetal Brain Female	brain
7	chr19:21264600-21266000	Active TSS	Fetal Intestine Small	intestine
8	chr19:21264600-21266200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:21264600-21266200	Active TSS	GM12878-XiMat	blood
10	chr19:21264800-21265800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:21264800-21265800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr19:21264800-21265800	Active TSS	Primary B cells from peripheral blood	blood
13	chr19:21264800-21265800	Active TSS	Primary T cells fromperipheralblood	blood
14	chr19:21264800-21265800	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr19:21264800-21265800	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr19:21264800-21265800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:21264800-21265800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:21264800-21265800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:21264800-21265800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:21264800-21265800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr19:21264800-21265800	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr19:21264800-21265800	Active TSS	Adipose Nuclei	Adipose
23	chr19:21264800-21265800	ZNF genes & repeats	Liver	Liver
24	chr19:21264800-21265800	Active TSS	Brain Cingulate Gyrus	brain
25	chr19:21264800-21265800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr19:21264800-21265800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:21264800-21265800	Active TSS	Brain Substantia Nigra	brain
28	chr19:21264800-21265800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr19:21264800-21265800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:21264800-21265800	Active TSS	Fetal Muscle Trunk	muscle
31	chr19:21264800-21265800	Active TSS	Fetal Muscle Leg	muscle
32	chr19:21264800-21265800	Active TSS	Placenta	Placenta
33	chr19:21264800-21265800	Active TSS	Fetal Stomach	stomach
34	chr19:21264800-21265800	Active TSS	Fetal Thymus	thymus
35	chr19:21264800-21265800	Active TSS	Placenta Amnion	Placenta Amnion
36	chr19:21264800-21265800	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr19:21264800-21265800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr19:21264800-21265800	Active TSS	Stomach Smooth Muscle	stomach
39	chr19:21264800-21265800	Active TSS	Hela-S3	cervix
40	chr19:21264800-21265800	Active TSS	K562	blood
41	chr19:21264800-21265800	Active TSS	NHEK	skin
42	chr19:21264800-21265800	Active TSS	NHLF	lung
43	chr19:21264800-21266000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr19:21264800-21266000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:21264800-21266000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:21264800-21266000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:21264800-21266000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:21264800-21266000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:21264800-21266000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:21264800-21266000	Active TSS	Brain Anterior Caudate	brain

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