Variant report

Variant	rs55936623
Chromosome Location	chr2:11887931-11887932
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	POLR2A	chr2:11886620-11891581	GM12878	blood:	n/a	n/a
2	MXI1	chr2:11886239-11888165	IMR90	lung:	n/a	n/a
3	POLR2A	chr2:11886473-11888191	GM18505	blood:	n/a	n/a
4	MXI1	chr2:11885917-11888799	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:11887886-11888510	K562	blood:	n/a	n/a
6	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
7	TEAD4	chr2:11887171-11887958	HepG2	liver:	n/a	n/a
8	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:11886625-11888663	MCF10A-Er-Src	breast:	n/a	n/a
10	KAT2A	chr2:11887881-11888007	GM12878	blood:	n/a	n/a
11	IRF1	chr2:11887332-11888156	K562	blood:	n/a	chr2:11888126-11888138 chr2:11887683-11887700
12	NR2F2	chr2:11887786-11888647	K562	blood:	n/a	n/a
13	POLR2A	chr2:11886585-11888855	K562	blood:	n/a	n/a
14	RAD21	chr2:11883135-11888795	SK-N-SH	brain:	n/a	chr2:11888754-11888767 chr2:11883562-11883572 chr2:11883630-11883644
15	MXI1	chr2:11886527-11889380	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:11887260-11891538	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:11886566-11891563	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11604255..11606398-chr2:11886112..11888104,2	K562	blood:
2	chr2:11886833..11889158-chr2:11909295..11910808,2	K562	blood:
3	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
4	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
5	chr2:11882508..11884186-chr2:11887506..11889026,2	MCF-7	breast:
6	chr2:10259345..10261058-chr2:11886635..11888299,2	K562	blood:
7	chr2:11885343..11888558-chr2:11916972..11921085,4	K562	blood:

Variant related genes	Relation type
ENSG00000230790	TF binding region
ENSG00000169016	Chromatin interaction
ENSG00000230790	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs59614513	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73917120	1.00[AMR][1000 genomes]
rs73917122	1.00[AMR][1000 genomes]
rs73917123	1.00[AMR][1000 genomes]
rs73917856	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11886000-11888000	Active TSS	Brain Germinal Matrix	brain
2	chr2:11886200-11888400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:11886200-11888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:11886400-11888000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:11886400-11888000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:11886400-11888000	Active TSS	HSMMtube	muscle
7	chr2:11886600-11888000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:11886600-11888000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:11886600-11888000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:11886600-11888000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:11886600-11888000	Active TSS	Esophagus	oesophagus
12	chr2:11886600-11888000	Active TSS	Left Ventricle	heart
13	chr2:11886600-11888000	Active TSS	Ovary	ovary
14	chr2:11886600-11888000	Active TSS	Right Atrium	heart
15	chr2:11886600-11888000	Active TSS	Right Ventricle	heart
16	chr2:11886600-11888000	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr2:11886600-11888000	Active TSS	GM12878-XiMat	blood
18	chr2:11886600-11888200	Active TSS	Psoas Muscle	Psoas
19	chr2:11886600-11888200	Active TSS	NHLF	lung
20	chr2:11886600-11888400	Active TSS	NHDF-Ad	bronchial
21	chr2:11886800-11888000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr2:11886800-11888000	Active TSS	Gastric	stomach
23	chr2:11886800-11888600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:11886800-11888800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:11887000-11888000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr2:11887000-11888400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:11887000-11888600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:11887000-11890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:11887000-11891600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:11887200-11888000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:11887200-11888000	Flanking Active TSS	Fetal Lung	lung
32	chr2:11887200-11888200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr2:11887200-11888200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr2:11887200-11888400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:11887200-11888400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr2:11887200-11888400	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr2:11887200-11888400	Flanking Active TSS	Liver	Liver
38	chr2:11887200-11888400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr2:11887200-11888400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr2:11887200-11888400	Flanking Active TSS	Fetal Thymus	thymus
41	chr2:11887200-11888400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr2:11887200-11888400	Flanking Active TSS	Dnd41	blood
43	chr2:11887200-11888600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr2:11887200-11888600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:11887200-11888600	Flanking Active TSS	NH-A	brain
46	chr2:11887200-11889200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr2:11887200-11889200	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr2:11887200-11889400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:11887200-11890400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr2:11887400-11888000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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