Variant report

Variant	rs1729980
Chromosome Location	chr3:98313156-98313157
allele	A/C
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	TBP	chr3:98311874-98313188	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:98311751-98313187	GM12878	blood:	n/a	n/a
3	NRF1	chr3:98311815-98313182	SK-N-SH	brain:	n/a	n/a
4	MAZ	chr3:98311726-98313168	IMR90	lung:	n/a	chr3:98312493-98312503
5	FOXA2	chr3:98312155-98313216	HepG2	liver:	n/a	n/a
6	TBP	chr3:98312291-98313188	K562	blood:	n/a	n/a
7	POLR2A	chr3:98312255-98313191	U87	brain:	n/a	n/a
8	POLR2A	chr3:98311705-98313193	GM12892	blood:	n/a	n/a
9	MXI1	chr3:98311171-98313210	IMR90	lung:	n/a	n/a
10	MTA3	chr3:98312500-98313179	GM12878	blood:	n/a	n/a
11	GATA1	chr3:98312252-98313191	K562	blood:	n/a	chr3:98312575-98312582 chr3:98312573-98312582 chr3:98312573-98312583 chr3:98312575-98312582 chr3:98312570-98312586 chr3:98312657-98312668 chr3:98312575-98312582
12	RCOR1	chr3:98312235-98313210	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98303079..98305719-chr3:98311231..98314146,3	K562	blood:
2	chr3:98311356..98313726-chr3:98530079..98532585,2	MCF-7	breast:
3	chr3:98303079..98306972-chr3:98311108..98314146,5	K562	blood:
4	chr3:98307277..98308985-chr3:98312690..98314425,2	K562	blood:

Variant related genes	Relation type
CPOX	TF binding region
ENSG00000080819	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10222524	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1350792	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1350793	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1381090	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675526	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675527	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675528	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675531	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1729978	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1729995	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2698315	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34330560	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762654	0.85[EUR][1000 genomes]
rs3853723	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4558798	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv536661	chr3:98286588-98315764	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98310000-98313200	Active TSS	Brain Hippocampus Middle	brain
2	chr3:98310600-98313200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:98310800-98313200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:98310800-98313200	Active TSS	Right Atrium	heart
5	chr3:98311000-98313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:98311000-98313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:98311000-98313200	Active TSS	Brain Germinal Matrix	brain
8	chr3:98311000-98313200	Active TSS	Esophagus	oesophagus
9	chr3:98311000-98313200	Active TSS	HSMM	muscle
10	chr3:98311200-98313200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:98311200-98313200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:98311400-98313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr3:98311400-98313200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:98311400-98313200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:98311400-98313200	Active TSS	Brain Cingulate Gyrus	brain
16	chr3:98311400-98313200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:98311400-98313200	Active TSS	Fetal Intestine Large	intestine
18	chr3:98311400-98313200	Active TSS	Right Ventricle	heart
19	chr3:98311400-98313200	Active TSS	A549	lung
20	chr3:98311400-98313200	Active TSS	HMEC	breast
21	chr3:98311400-98313200	Active TSS	NHLF	lung
22	chr3:98311600-98313200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:98311600-98313200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:98311600-98313200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:98311600-98313200	Active TSS	Psoas Muscle	Psoas
26	chr3:98311600-98313200	Active TSS	Thymus	Thymus
27	chr3:98311600-98313200	Active TSS	Hela-S3	cervix
28	chr3:98311800-98313200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:98311800-98313200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:98311800-98313200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:98311800-98313200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:98311800-98313200	Active TSS	Brain Anterior Caudate	brain
33	chr3:98311800-98313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:98311800-98313200	Active TSS	Fetal Brain Female	brain
35	chr3:98311800-98313200	Active TSS	Rectal Smooth Muscle	rectum
36	chr3:98311800-98313200	Active TSS	Stomach Smooth Muscle	stomach
37	chr3:98312000-98313200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:98312000-98313200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:98312000-98313200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:98312000-98313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:98312000-98313200	Active TSS	Colonic Mucosa	Colon
42	chr3:98312000-98313200	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:98312000-98313200	Active TSS	Osteobl	bone
44	chr3:98312200-98313200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:98312600-98313200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr3:98312600-98313200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr3:98312600-98313200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:98312600-98313200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:98312600-98313200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:98312600-98313200	Flanking Active TSS	Fetal Thymus	thymus

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