Variant report

Variant	rs648818
Chromosome Location	chr2:234755402-234755403
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	chr2:234755012-234756080	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:234755055-234755860	K562	blood:	n/a	n/a
3	POLR2A	chr2:234755154-234760215	U87	brain:	n/a	n/a
4	POLR2A	chr2:234755022-234759760	K562	blood:	n/a	n/a
5	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
6	POLR2A	chr2:234754982-234760241	PANC-1	pancreas:	n/a	n/a
7	SPI1	chr2:234755111-234755457	HL-60	blood:	n/a	chr2:234755247-234755260 chr2:234755249-234755258 chr2:234755248-234755261
8	POLR2A	chr2:234755081-234755509	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:234755076-234756113	K562	blood:	n/a	n/a
10	SPI1	chr2:234755136-234755418	HL-60	blood:	n/a	chr2:234755247-234755260 chr2:234755249-234755258 chr2:234755248-234755261
11	POLR2A	chr2:234755286-234756253	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:234755167-234759670	A549	lung:	n/a	n/a
13	POLR2A	chr2:234755123-234755559	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr2:234755017-234760215	U87	brain:	n/a	n/a
15	SPI1	chr2:234755091-234755422	GM12891	blood:	n/a	chr2:234755247-234755260 chr2:234755249-234755258 chr2:234755248-234755261
16	POLR2A	chr2:234755083-234756511	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234755244..234757143-chr2:234762255..234764795,3	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12692249	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs169922	0.87[ASN][1000 genomes]
rs169925	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]
rs183331	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs213545	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2286433	1.00[CEU][hapmap]
rs2302156	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4663339	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs501145	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs503913	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[YRI][hapmap]
rs525359	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs528971	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531643	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs554699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556691	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs580045	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs609942	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs619929	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs626110	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs637082	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs638071	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6431643	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6431644	0.87[ASN][1000 genomes]
rs650570	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs650700	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs654279	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689101	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7570755	0.92[CEU][hapmap]
rs887062	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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

No data

Chromatin state (count:86 , 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	chr2:234743800-234759800	Strong transcription	Osteobl	bone
35	chr2:234744000-234760400	Strong transcription	K562	blood
36	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
37	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
38	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:234748000-234759200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
42	chr2:234748200-234758400	Strong transcription	Fetal Thymus	thymus
43	chr2:234748200-234759000	Genic enhancers	Dnd41	blood
44	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:234748800-234756600	Strong transcription	HSMM	muscle
48	chr2:234748800-234757600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:234749000-234756200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:234749000-234758200	Strong transcription	Primary hematopoietic stem cells	blood

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