Variant report

Variant	rs2164460
Chromosome Location	chr1:224920550-224920551
allele	C/T
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	NR2F2	chr1:224919833-224920616	MCF-7	breast:	n/a	n/a
2	RELA	chr1:224920506-224921505	GM12878	blood:	n/a	n/a
3	EP300	chr1:224920469-224921943	GM12878	blood:	n/a	n/a
4	IKZF1	chr1:224920525-224921635	GM12878	blood:	n/a	n/a
5	IRF3	chr1:224920438-224920629	GM12878	blood:	n/a	n/a
6	WRNIP1	chr1:224920309-224922464	GM12878	blood:	n/a	n/a
7	RELA	chr1:224920305-224921679	GM18951	blood:	n/a	n/a
8	MAX	chr1:224920495-224921875	GM12878	blood:	n/a	chr1:224921619-224921630
9	MXI1	chr1:224920533-224921795	GM12878	blood:	n/a	n/a
10	RCOR1	chr1:224920522-224921833	GM12878	blood:	n/a	n/a
11	STAT1	chr1:224920455-224921417	GM12878	blood:	n/a	chr1:224921237-224921249 chr1:224920477-224920485
12	NR2F2	chr1:224919952-224920630	MCF-7	breast:	n/a	n/a
13	ZNF384	chr1:224920487-224921039	GM12878	blood:	n/a	n/a
14	EBF1	chr1:224920381-224922593	GM12878	blood:	n/a	chr1:224921507-224921518 chr1:224921508-224921517 chr1:224921541-224921554 chr1:224921543-224921553 chr1:224921541-224921552 chr1:224921543-224921552 chr1:224921543-224921552
15	SMC3	chr1:224920410-224921757	GM12878	blood:	n/a	n/a
16	ZNF143	chr1:224920549-224921466	GM12878	blood:	n/a	n/a
17	TBP	chr1:224920496-224921847	GM12878	blood:	n/a	n/a
18	CHD2	chr1:224920202-224921848	GM12878	blood:	n/a	n/a
19	STAT3	chr1:224920538-224921730	GM12878	blood:	n/a	chr1:224921237-224921249
20	TBL1XR1	chr1:224920319-224921816	GM12878	blood:	n/a	n/a
21	CUX1	chr1:224920541-224921790	GM12878	blood:	n/a	n/a
22	MAZ	chr1:224920514-224921813	GM12878	blood:	n/a	chr1:224921619-224921630
23	USF2	chr1:224920443-224921244	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:224920216..224922830-chr1:225115922..225118673,2	MCF-7	breast:
2	chr1:224920081..224922903-chr1:224922930..224927181,4	MCF-7	breast:
3	chr1:224912065..224916127-chr1:224919460..224922896,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229400	TF binding region
ENSG00000185842	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10915712	1.00[AMR][1000 genomes]
rs73129827	1.00[AMR][1000 genomes]
rs892976	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524125	chr1:224902054-225021860	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224914800-224924400	Weak transcription	Ovary	ovary
2	chr1:224915000-224924400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224915400-224920800	Weak transcription	Spleen	Spleen
4	chr1:224915400-224921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:224915600-224921200	Weak transcription	Dnd41	blood
6	chr1:224915800-224921000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:224916000-224921000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:224916000-224921000	Weak transcription	NH-A	brain
9	chr1:224916200-224921400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:224916200-224924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:224917400-224921600	Enhancers	NHDF-Ad	bronchial
12	chr1:224918200-224921800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:224918400-224924600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:224919000-224923200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:224919200-224920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:224919400-224920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:224919400-224921000	Weak transcription	NHLF	lung
18	chr1:224919600-224926200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:224919800-224921200	Enhancers	Hela-S3	cervix
20	chr1:224919800-224921400	Enhancers	HepG2	liver
21	chr1:224919800-224921600	Enhancers	Pancreas	Pancrea
22	chr1:224919800-224921800	Enhancers	Esophagus	oesophagus
23	chr1:224919800-224921800	Enhancers	Fetal Intestine Small	intestine
24	chr1:224919800-224922400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:224919800-224922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:224920000-224921600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:224920000-224921800	Enhancers	HMEC	breast
28	chr1:224920000-224922200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:224920200-224921000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:224920200-224921000	Enhancers	Psoas Muscle	Psoas
31	chr1:224920200-224921200	Enhancers	Gastric	stomach
32	chr1:224920200-224921400	Enhancers	Stomach Mucosa	stomach
33	chr1:224920200-224921600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:224920200-224921600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:224920200-224921600	Enhancers	Adipose Nuclei	Adipose
36	chr1:224920200-224921600	Enhancers	Fetal Intestine Large	intestine
37	chr1:224920200-224921800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:224920200-224921800	Enhancers	Right Atrium	heart
39	chr1:224920200-224921800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:224920200-224921800	Enhancers	Osteobl	bone
41	chr1:224920200-224922000	Enhancers	Right Ventricle	heart
42	chr1:224920200-224922400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:224920200-224923400	Enhancers	Fetal Thymus	thymus
44	chr1:224920200-224924200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:224920200-224925000	Weak transcription	Colonic Mucosa	Colon
46	chr1:224920400-224920600	Flanking Active TSS	Liver	Liver
47	chr1:224920400-224921000	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr1:224920400-224921200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr1:224920400-224921400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:224920400-224921400	Enhancers	HUES48 Cell Line	embryonic stem cell

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