Variant report

Variant	rs169925
Chromosome Location	chr2:234753008-234753009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234752792-234753807	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:234752789-234753104	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:234752773-234753889	K562	blood:	n/a	n/a
4	POLR2A	chr2:234751826-234753837	U87	brain:	n/a	n/a
5	POLR2A	chr2:234752734-234753122	A549	lung:	n/a	n/a
6	POLR2A	chr2:234752662-234753027	A549	lung:	n/a	n/a
7	POLR2A	chr2:234752930-234753064	A549	lung:	n/a	n/a
8	POLR2A	chr2:234751938-234753676	PBDE	blood:	n/a	n/a
9	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
10	POLR2A	chr2:234752775-234754117	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:234751629-234753843	U87	brain:	n/a	n/a
12	POLR2A	chr2:234752821-234753210	K562	blood:	n/a	n/a
13	POLR2A	chr2:234752868-234753632	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:234752697-234753255	K562	blood:	n/a	n/a
15	POLR2A	chr2:234752732-234753237	GM12892	blood:	n/a	n/a
16	POLR2A	chr2:234751698-234753878	K562	blood:	n/a	n/a
17	POLR2A	chr2:234752784-234753197	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:234751728-234753879	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr2:234752901-234753064	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:234751853-234753778	A549	lung:	n/a	n/a
21	POLR2A	chr2:234753001-234753070	MCF-7	breast:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12692249	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs169922	0.86[ASN][1000 genomes]
rs183331	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs213545	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2286433	0.96[CEU][hapmap]
rs2302156	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs4663339	0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs501145	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs503913	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs525359	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs528971	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531643	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554699	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556691	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs580045	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs609942	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs619929	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs626110	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs637082	0.97[EUR][1000 genomes]
rs638071	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs6431643	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6431644	0.86[ASN][1000 genomes]
rs648818	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs650570	0.95[EUR][1000 genomes]
rs650700	0.97[EUR][1000 genomes]
rs654279	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs689101	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7570755	0.87[CEU][hapmap]
rs887062	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs169925	NCL	cis	parietal	SCAN
rs169925	SNORD20	cis	cerebellum	SCAN
rs169925	CAB39	cis	parietal	SCAN

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	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
4	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:234741200-234759800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:234741800-234762000	Weak transcription	Gastric	stomach
8	chr2:234742000-234759600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:234742200-234759400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:234742200-234760400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:234742600-234759600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:234742600-234759800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:234742600-234760400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:234742600-234760600	Strong transcription	NHEK	skin
17	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr2:234742800-234759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:234742800-234760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:234743000-234758600	Strong transcription	Fetal Intestine Large	intestine
24	chr2:234743000-234759400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:234743000-234760000	Strong transcription	HMEC	breast
27	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:234743400-234759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:234743600-234754000	Strong transcription	Fetal Intestine Small	intestine
35	chr2:234743800-234759800	Strong transcription	Osteobl	bone
36	chr2:234744000-234753800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:234744000-234760400	Strong transcription	K562	blood
38	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
39	chr2:234744200-234755400	Weak transcription	Fetal Brain Male	brain
40	chr2:234744600-234753600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
42	chr2:234747000-234753200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:234747000-234753800	Strong transcription	NHLF	lung
44	chr2:234747200-234754200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:234748000-234759200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
49	chr2:234748200-234758400	Strong transcription	Fetal Thymus	thymus
50	chr2:234748200-234759000	Genic enhancers	Dnd41	blood

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