Variant report

Variant	rs28948394
Chromosome Location	chr2:234764794-234764795
allele	C/G/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	chr2:234761541-234765493	PBDE	blood:	n/a	n/a
2	SP1	chr2:234764779-234765097	GM12878	blood:	n/a	n/a
3	GATA1	chr2:234764677-234766915	PBDE	blood:	n/a	chr2:234766186-234766193 chr2:234766408-234766419 chr2:234766688-234766695
4	NFYA	chr2:234764768-234765115	Hela-S3	cervix:	n/a	chr2:234764991-234765009
5	SP1	chr2:234764765-234765152	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr2:234764787-234765105	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234287841..234290274-chr2:234763393..234765427,2	MCF-7	breast:
2	chr2:234763499..234765002-chr2:234766647..234768306,2	MCF-7	breast:
3	chr2:234764614..234767781-chr2:234770318..234773555,4	MCF-7	breast:
4	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000201013	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28900714	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28900723	0.98[ASN][1000 genomes]
rs28900724	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28900978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28901606	0.86[ASN][1000 genomes]
rs28902471	0.93[ASN][1000 genomes]
rs3771333	0.91[ASN][1000 genomes]
rs56262514	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs58339824	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60573749	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73118753	1.00[AMR][1000 genomes];0.91[ASN][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234763600-234776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:234763800-234765000	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:234763800-234766000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:234763800-234766000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:234763800-234766200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:234763800-234774600	Weak transcription	Placenta	Placenta
7	chr2:234763800-234774800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:234763800-234775200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:234763800-234775400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:234763800-234776600	Weak transcription	Right Ventricle	heart
11	chr2:234764000-234764800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:234764000-234765800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:234764000-234766000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:234764000-234766000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:234764000-234766000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:234764000-234766000	Weak transcription	Stomach Mucosa	stomach
17	chr2:234764000-234766000	Enhancers	K562	blood
18	chr2:234764000-234766000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:234764000-234766200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:234764000-234774400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:234764000-234775200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:234764000-234776400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:234764000-234776600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:234764000-234776600	Weak transcription	HUVEC	blood vessel
25	chr2:234764200-234764800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:234764200-234766000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:234764200-234766000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:234764200-234766000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:234764200-234766000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:234764200-234766000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:234764200-234766200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:234764200-234766200	Weak transcription	Thymus	Thymus
33	chr2:234764200-234766400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:234764200-234766400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:234764200-234766400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:234764200-234766400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:234764200-234766400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:234764200-234766400	Weak transcription	GM12878-XiMat	blood
39	chr2:234764200-234770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:234764200-234771000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:234764200-234773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:234764200-234774200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:234764200-234774400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:234764200-234774600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:234764200-234774800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:234764200-234774800	Weak transcription	Osteobl	bone
47	chr2:234764200-234775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:234764200-234775200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:234764200-234776600	Weak transcription	Primary B cells from cord blood	blood
50	chr2:234764200-234776600	Weak transcription	Primary T cells from cord blood	blood

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