Variant report

Variant	rs12976796
Chromosome Location	chr19:21204433-21204434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21203269..21205162-chr19:21263863..21266449,2	MCF-7	breast:
2	chr19:21203226..21204874-chr19:21207837..21209473,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160352	Chromatin interaction
ENSG00000271598	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10401931	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10409844	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10412267	0.80[ASN][1000 genomes]
rs10412688	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413175	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10413692	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413983	0.80[ASN][1000 genomes]
rs10414134	0.80[ASN][1000 genomes]
rs10417165	0.95[ASN][1000 genomes]
rs10418706	0.97[ASN][1000 genomes]
rs10421819	0.82[ASN][1000 genomes]
rs10422193	0.91[ASN][1000 genomes]
rs10424283	0.80[ASN][1000 genomes]
rs10425969	0.83[ASN][1000 genomes]
rs11085424	0.95[ASN][1000 genomes]
rs11085431	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11666640	0.83[ASN][1000 genomes]
rs11666869	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11668335	0.81[EUR][1000 genomes]
rs11669248	0.93[EUR][1000 genomes]
rs11670162	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11671894	0.95[ASN][1000 genomes]
rs11672142	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12104220	0.80[ASN][1000 genomes]
rs12104387	0.98[ASN][1000 genomes]
rs12608706	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12608931	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609005	0.83[ASN][1000 genomes]
rs12609167	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12609427	0.95[EUR][1000 genomes]
rs12609510	0.95[ASN][1000 genomes]
rs12609831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12973640	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12975789	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];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1609441	0.80[ASN][1000 genomes]
rs1968523	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1971054	0.81[EUR][1000 genomes]
rs1971815	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2013048	0.80[ASN][1000 genomes]
rs2081050	0.94[ASN][1000 genomes]
rs2081052	0.88[ASN][1000 genomes]
rs2081054	0.98[ASN][1000 genomes]
rs2081055	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081056	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081057	0.98[ASN][1000 genomes]
rs2098681	0.97[ASN][1000 genomes]
rs2099648	0.97[ASN][1000 genomes]
rs2112803	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2164988	0.85[ASN][1000 genomes]
rs2164989	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2358792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884548	0.98[ASN][1000 genomes]
rs2884554	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255903	0.98[ASN][1000 genomes]
rs4292035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4365405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4488591	0.80[ASN][1000 genomes]
rs4808273	0.87[ASN][1000 genomes]
rs4809119	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62122564	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62122565	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511175	0.88[ASN][1000 genomes]
rs6511179	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511181	0.94[ASN][1000 genomes]
rs6511183	0.83[ASN][1000 genomes]
rs6511184	0.83[ASN][1000 genomes]
rs6511186	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6511187	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511188	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6511191	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7246723	0.80[ASN][1000 genomes]
rs7247413	0.95[ASN][1000 genomes]
rs7247553	0.97[ASN][1000 genomes]
rs7248087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249283	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7249736	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7250169	0.80[ASN][1000 genomes]
rs7250274	0.86[AFR][1000 genomes]
rs7252277	0.95[ASN][1000 genomes]
rs7253530	0.95[ASN][1000 genomes]
rs7254047	0.80[ASN][1000 genomes]
rs7254722	0.92[ASN][1000 genomes]
rs7254768	0.97[ASN][1000 genomes]
rs7257481	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7258195	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7258409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7258477	0.98[ASN][1000 genomes]
rs7258831	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7259653	0.98[ASN][1000 genomes]
rs7260268	0.80[ASN][1000 genomes]
rs7260600	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7343175	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8100289	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8100599	0.80[ASN][1000 genomes]
rs8101412	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8101461	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8102966	0.98[ASN][1000 genomes]
rs8103696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106801	0.80[ASN][1000 genomes]
rs8107638	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8107982	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8109549	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8109577	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8112054	0.83[ASN][1000 genomes]
rs8112216	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8113541	0.87[AFR][1000 genomes]
rs9304980	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9941463	0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12976796	ZNF714	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21202800-21204600	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr19:21202800-21204800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr19:21202800-21204800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:21202800-21204800	Active TSS	Stomach Smooth Muscle	stomach
5	chr19:21203000-21204600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:21203000-21204600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:21203000-21204600	Active TSS	Brain Cingulate Gyrus	brain
8	chr19:21203000-21204600	Active TSS	Brain Hippocampus Middle	brain
9	chr19:21203000-21204600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr19:21203000-21204600	Active TSS	Fetal Intestine Large	intestine
11	chr19:21203000-21204600	Active TSS	Fetal Intestine Small	intestine
12	chr19:21203000-21204600	Active TSS	Fetal Muscle Leg	muscle
13	chr19:21203000-21204600	Active TSS	Right Atrium	heart
14	chr19:21203000-21204600	Active TSS	NH-A	brain
15	chr19:21203000-21204600	Active TSS	NHDF-Ad	bronchial
16	chr19:21203000-21204800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:21203000-21204800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:21203000-21204800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:21203000-21204800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:21203000-21204800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:21203000-21204800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:21203000-21204800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:21203000-21204800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:21203000-21204800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr19:21203000-21204800	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr19:21203000-21204800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:21203000-21204800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:21203000-21204800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:21203000-21204800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:21203000-21204800	Active TSS	Fetal Lung	lung
31	chr19:21203000-21204800	Active TSS	Ovary	ovary
32	chr19:21203000-21204800	Active TSS	HMEC	breast
33	chr19:21203000-21204800	Active TSS	K562	blood
34	chr19:21203000-21204800	Active TSS	Osteobl	bone
35	chr19:21203000-21205000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:21203000-21205000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr19:21203000-21205000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:21203000-21205000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:21203000-21205000	Active TSS	Brain Anterior Caudate	brain
40	chr19:21203000-21205000	Active TSS	Brain Germinal Matrix	brain
41	chr19:21203000-21205000	Active TSS	Fetal Brain Female	brain
42	chr19:21203000-21205000	Active TSS	Fetal Kidney	kidney
43	chr19:21203000-21205000	Active TSS	HSMM	muscle
44	chr19:21203000-21205200	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:21203000-21205400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:21203000-21205400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:21203000-21205400	Active TSS	GM12878-XiMat	blood
48	chr19:21203000-21205400	Active TSS	HSMMtube	muscle
49	chr19:21203000-21205600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:21203000-21206200	Active TSS	NHLF	lung

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