Variant report

Variant	rs28900709
Chromosome Location	chr2:234752656-234752657
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	POLR2A	chr2:234751826-234753837	U87	brain:	n/a	n/a
2	POLR2A	chr2:234751938-234753676	PBDE	blood:	n/a	n/a
3	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
4	POLR2A	chr2:234751629-234753843	U87	brain:	n/a	n/a
5	POLR2A	chr2:234751698-234753878	K562	blood:	n/a	n/a
6	POLR2A	chr2:234751728-234753879	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr2:234751853-234753778	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234747493..234750001-chr2:234750667..234752950,3	MCF-7	breast:
2	chr2:234751005..234753072-chr2:234754177..234756190,2	MCF-7	breast:

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11563217	1.00[AMR][1000 genomes]
rs11890045	1.00[AMR][1000 genomes]
rs1392605	1.00[AMR][1000 genomes]
rs1500478	1.00[AMR][1000 genomes]
rs28900717	1.00[AMR][1000 genomes]
rs28901624	1.00[AMR][1000 genomes]
rs28901648	1.00[AMR][1000 genomes]
rs28902171	1.00[AMR][1000 genomes]
rs28902178	1.00[AMR][1000 genomes]
rs28902477	1.00[AMR][1000 genomes]
rs28946906	1.00[AMR][1000 genomes]
rs61415915	1.00[AMR][1000 genomes]
rs61650568	1.00[AMR][1000 genomes]
rs73110898	1.00[AMR][1000 genomes]
rs73112612	1.00[AMR][1000 genomes]
rs73112625	1.00[AMR][1000 genomes]
rs73112628	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1008316	chr2:234728911-234758539	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234739800-234752800	Weak transcription	Spleen	Spleen
4	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
5	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
7	chr2:234741200-234759800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:234741800-234762000	Weak transcription	Gastric	stomach
9	chr2:234742000-234759600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:234742200-234759400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:234742200-234760400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:234742600-234759600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:234742600-234759800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:234742600-234760400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:234742600-234760600	Strong transcription	NHEK	skin
18	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr2:234742800-234759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:234742800-234760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:234743000-234758600	Strong transcription	Fetal Intestine Large	intestine
25	chr2:234743000-234759400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:234743000-234760000	Strong transcription	HMEC	breast
28	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:234743400-234759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:234743600-234754000	Strong transcription	Fetal Intestine Small	intestine
36	chr2:234743800-234759800	Strong transcription	Osteobl	bone
37	chr2:234744000-234753800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:234744000-234760400	Strong transcription	K562	blood
39	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
40	chr2:234744200-234755400	Weak transcription	Fetal Brain Male	brain
41	chr2:234744600-234753600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
43	chr2:234747000-234753200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:234747000-234753800	Strong transcription	NHLF	lung
45	chr2:234747200-234754200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:234747400-234753000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:234748000-234759200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach

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