Variant report

Variant	rs13424092
Chromosome Location	chr2:180132937-180132938
allele	C/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	EP300	chr2:180132920-180133599	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr2:180132833-180133684	MCF-7	breast:	n/a	n/a
3	SP1	chr2:180132876-180133569	A549	lung:	n/a	n/a
4	PML	chr2:180132802-180133406	GM12878	blood:	n/a	n/a
5	NFATC1	chr2:180132885-180133395	GM12878	blood:	n/a	n/a
6	FOXM1	chr2:180132849-180133488	GM12878	blood:	n/a	n/a
7	NFIC	chr2:180132677-180133490	GM12878	blood:	n/a	n/a
8	FOXM1	chr2:180132880-180133524	GM12878	blood:	n/a	n/a
9	MEF2A	chr2:180132787-180133407	GM12878	blood:	n/a	chr2:180132994-180133005 chr2:180133024-180133045 chr2:180132992-180133007 chr2:180132963-180132984 chr2:180133028-180133039 chr2:180132993-180133007
10	MEF2C	chr2:180132827-180133375	GM12878	blood:	n/a	chr2:180132994-180133005 chr2:180133024-180133045 chr2:180132992-180133007 chr2:180132963-180132984 chr2:180133028-180133039 chr2:180132993-180133007
11	TFAP2C	chr2:180132857-180134020	Hela-S3	cervix:	n/a	chr2:180133241-180133256
12	ATF2	chr2:180132917-180133336	GM12878	blood:	n/a	n/a
13	CEBPB	chr2:180132929-180133495	MCF-7	breast:	n/a	n/a
14	NFIC	chr2:180132731-180133429	GM12878	blood:	n/a	n/a
15	ATF2	chr2:180132865-180133290	GM12878	blood:	n/a	n/a
16	IKZF1	chr2:180132860-180133465	GM12878	blood:	n/a	n/a
17	MEF2A	chr2:180132786-180133351	GM12878	blood:	n/a	chr2:180132994-180133005 chr2:180133024-180133045 chr2:180132992-180133007 chr2:180132963-180132984 chr2:180133028-180133039 chr2:180132993-180133007
18	TCF12	chr2:180132833-180133696	A549	lung:	n/a	n/a
19	RUNX3	chr2:180132731-180133405	GM12878	blood:	n/a	n/a
20	GATA3	chr2:180132844-180133694	MCF-7	breast:	n/a	n/a
21	EP300	chr2:180132881-180133618	A549	lung:	n/a	n/a
22	MTA3	chr2:180132853-180133383	GM12878	blood:	n/a	n/a
23	SP1	chr2:180132844-180133559	A549	lung:	n/a	n/a
24	IRF4	chr2:180132907-180133368	GM12878	blood:	n/a	n/a
25	GATA3	chr2:180132894-180133746	MCF-7	breast:	n/a	n/a
26	FOSL1	chr2:180132906-180133602	HCT-116	colon:	n/a	chr2:180133044-180133056
27	RUNX3	chr2:180132802-180133329	GM12878	blood:	n/a	n/a
28	TFAP2A	chr2:180132917-180133668	Hela-S3	cervix:	n/a	chr2:180133243-180133258
29	FOSL2	chr2:180132885-180133555	A549	lung:	n/a	chr2:180133044-180133056

No.	Distal block	Cell Line	Cell type
1	chr2:180129872..180132234-chr2:180132866..180134594,2	K562	blood:
2	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
3	chr2:180127197..180131104-chr2:180131643..180133525,5	MCF-7	breast:
4	chr2:180132248..180134762-chr2:180137452..180139078,2	MCF-7	breast:

Variant related genes	Relation type
SESTD1	TF binding region
ENSG00000237477	Chromatin interaction
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10176828	1.00[CHB][hapmap]
rs10208882	1.00[CHB][hapmap]
rs10209875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10221811	1.00[CHB][hapmap]
rs12613089	1.00[CHB][hapmap]
rs12616452	1.00[CHB][hapmap]
rs12618724	0.80[ASN][1000 genomes]
rs13383806	1.00[CHB][hapmap]
rs13387502	0.80[ASN][1000 genomes]
rs13395559	1.00[CHB][hapmap]
rs13408774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13417112	0.89[ASN][1000 genomes]
rs13422693	1.00[CHB][hapmap]
rs13429191	0.80[ASN][1000 genomes]
rs16866647	1.00[CHB][hapmap]
rs35041512	0.89[ASN][1000 genomes]
rs7578417	1.00[CHB][hapmap]
rs7588135	1.00[CHB][hapmap]
rs7608106	1.00[CHB][hapmap]
rs9288024	1.00[CHB][hapmap]

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	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:180130000-180135200	Weak transcription	Brain Angular Gyrus	brain
3	chr2:180130000-180137200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:180130000-180138000	Weak transcription	Gastric	stomach
5	chr2:180130000-180138200	Weak transcription	Aorta	Aorta
6	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:180130200-180133000	Weak transcription	A549	lung
12	chr2:180130200-180133000	Weak transcription	NHDF-Ad	bronchial
13	chr2:180130200-180133200	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:180130200-180136200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:180130200-180137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:180130200-180137200	Weak transcription	NH-A	brain
17	chr2:180130400-180133000	Weak transcription	Brain Substantia Nigra	brain
18	chr2:180130400-180133200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:180130400-180136000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:180130400-180137400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:180130600-180133000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:180130600-180138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:180130800-180133000	Weak transcription	Adipose Nuclei	Adipose
26	chr2:180130800-180133200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:180130800-180135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:180131000-180133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:180131000-180133200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:180131200-180133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:180131200-180133200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:180132200-180134200	Enhancers	Hela-S3	cervix
33	chr2:180132600-180133400	Enhancers	GM12878-XiMat	blood
34	chr2:180132600-180133600	Enhancers	Placenta	Placenta
35	chr2:180132600-180133600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr2:180132600-180133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:180132600-180134000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:180132600-180134000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:180132600-180134000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:180132600-180134000	Enhancers	HepG2	liver
41	chr2:180132600-180134000	Enhancers	NHEK	skin
42	chr2:180132600-180134600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:180132800-180133600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr2:180132800-180133600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:180132800-180133600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:180132800-180133800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:180132800-180133800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:180132800-180133800	Enhancers	HUVEC	blood vessel
49	chr2:180132800-180133800	Enhancers	Osteobl	bone
50	chr2:180132800-180134000	Enhancers	Muscle Satellite Cultured Cells	--

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