Variant report

Variant	rs56179735
Chromosome Location	chr3:23853119-23853120
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	PML	chr3:23852317-23853162	GM12878	blood:	n/a	n/a
2	MYC	chr3:23851740-23853276	MCF10A-Er-Src	breast:	n/a	chr3:23852128-23852138 chr3:23852246-23852256
3	HA-E2F1	chr3:23851757-23853129	MCF-7	breast:	n/a	chr3:23852153-23852160 chr3:23852152-23852163 chr3:23852128-23852137 chr3:23852153-23852160 chr3:23852152-23852162 chr3:23852153-23852161 chr3:23852205-23852214 chr3:23852153-23852160 chr3:23852247-23852256 chr3:23852153-23852164 chr3:23852153-23852161
4	IRF1	chr3:23852787-23853287	K562	blood:	n/a	chr3:23853235-23853249
5	MYC	chr3:23852710-23853250	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD1	chr3:23850909-23853708	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23850301..23853237-chr3:23957517..23960615,4	MCF-7	breast:
2	chr3:23852479..23855481-chr3:23956917..23960502,4	MCF-7	breast:
3	chr3:23851889..23854305-chr3:24536164..24537886,2	K562	blood:

Variant related genes	Relation type
UBE2E1-AS1	TF binding region
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs34398194	0.84[EUR][1000 genomes]
rs55712541	0.94[EUR][1000 genomes]
rs55825200	0.94[EUR][1000 genomes]
rs55904513	0.84[EUR][1000 genomes]
rs56222205	0.94[EUR][1000 genomes]
rs60267670	0.89[EUR][1000 genomes]
rs73034788	0.84[EUR][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834637	chr3:23703928-23886144	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23849800-23855400	Weak transcription	Hela-S3	cervix
2	chr3:23850000-23854600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:23850000-23856400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:23850800-23853200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr3:23850800-23853200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:23851200-23853400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr3:23851600-23853200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:23851600-23853200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:23851600-23853800	Active TSS	GM12878-XiMat	blood
10	chr3:23851800-23853200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:23851800-23853200	Active TSS	Fetal Kidney	kidney
12	chr3:23852000-23853200	Active TSS	Fetal Intestine Small	intestine
13	chr3:23852000-23853200	Active TSS	Right Ventricle	heart
14	chr3:23852000-23853200	Active TSS	Thymus	Thymus
15	chr3:23852000-23853400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:23852000-23855000	Strong transcription	Dnd41	blood
17	chr3:23852600-23853200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:23852600-23853200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:23852600-23853200	Flanking Active TSS	Fetal Thymus	thymus
20	chr3:23852600-23853200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:23852600-23853200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr3:23852600-23853200	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:23852600-23853200	Flanking Active TSS	HMEC	breast
24	chr3:23852600-23853200	Flanking Active TSS	HUVEC	blood vessel
25	chr3:23852600-23853400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:23852600-23853400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:23852600-23853400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:23852600-23853400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr3:23852600-23853600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:23852800-23853200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:23852800-23853200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr3:23852800-23853200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr3:23852800-23853200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr3:23852800-23853200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:23852800-23853200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:23852800-23853200	Flanking Active TSS	Liver	Liver
37	chr3:23852800-23853200	Enhancers	Brain Germinal Matrix	brain
38	chr3:23852800-23853200	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr3:23852800-23853600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:23852800-23853600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr3:23852800-23853600	Transcr. at gene 5' and 3'	K562	blood
42	chr3:23852800-23854400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:23852800-23859600	Weak transcription	Gastric	stomach
44	chr3:23853000-23853200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:23853000-23853200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:23853000-23853200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:23853000-23853200	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr3:23853000-23853200	Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr3:23853000-23853200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:23853000-23853200	Enhancers	Brain Substantia Nigra	brain

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