Variant report

Variant	rs609942
Chromosome Location	chr2:234763755-234763756
allele	C/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	FOXM1	chr2:234762589-234763888	ECC-1	luminal epithelium:	n/a	n/a
2	SP1	chr2:234762785-234763935	HCT-116	colon:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234762872-234762886 chr2:234763236-234763257 chr2:234763215-234763226
3	POLR2A	chr2:234762944-234764240	IMR90	lung:	n/a	n/a
4	MXI1	chr2:234762986-234763867	GM12878	blood:	n/a	n/a
5	GABPA	chr2:234763037-234763757	HL-60	blood:	n/a	n/a
6	ELK4	chr2:234763171-234763902	Hela-S3	cervix:	n/a	n/a
7	GATA1	chr2:234762999-234764180	PBDE	blood:	n/a	chr2:234763473-234763490
8	POLR2A	chr2:234762824-234763828	ProgFib	skin:	n/a	n/a
9	E2F4	chr2:234760995-234764094	MCF10A-Er-Src	breast:	n/a	chr2:234762623-234762633
10	FOSL2	chr2:234762960-234763925	A549	lung:	n/a	n/a
11	MXI1	chr2:234761711-234763997	IMR90	lung:	n/a	n/a
12	MAX	chr2:234761813-234763874	A549	lung:	n/a	n/a
13	KAP1	chr2:234763207-234763865	U2OS	brain:	n/a	n/a
14	CBX3	chr2:234763144-234763777	K562	blood:	n/a	n/a
15	SIN3AK20	chr2:234762874-234763861	A549	lung:	n/a	n/a
16	TAF1	chr2:234762764-234763876	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:234762874-234763780	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr2:234761405-234764492	PANC-1	pancreas:	n/a	n/a
19	MAX	chr2:234762801-234763801	HepG2	liver:	n/a	n/a
20	RCOR1	chr2:234762996-234764047	K562	blood:	n/a	n/a
21	SIN3A	chr2:234762064-234763814	H1-hESC	embryonic stem cell:	n/a	chr2:234763530-234763543
22	MXI1	chr2:234761803-234764274	SK-N-SH	brain:	n/a	n/a
23	SIN3AK20	chr2:234762676-234763767	MCF-7	breast:	n/a	n/a
24	TCF12	chr2:234762822-234763799	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr2:234763193-234764077	K562	blood:	n/a	n/a
26	POLR2A	chr2:234762287-234763857	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOXM1	chr2:234762852-234763783	SK-N-SH	brain:	n/a	n/a
28	GABPA	chr2:234762628-234763919	MCF-7	breast:	n/a	n/a
29	SP1	chr2:234762785-234763791	A549	lung:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234762872-234762886 chr2:234763236-234763257 chr2:234763215-234763226
30	POLR2A	chr2:234761541-234765493	PBDE	blood:	n/a	n/a
31	TCF12	chr2:234762621-234764407	A549	lung:	n/a	chr2:234762771-234762781
32	POLR2A	chr2:234761604-234763892	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr2:234762429-234763825	HCT-116	colon:	n/a	n/a
34	POLR2A	chr2:234761661-234764178	K562	blood:	n/a	n/a
35	GATA2	chr2:234763262-234763768	HUVEC	blood vessel:	n/a	chr2:234763473-234763490
36	TAL1	chr2:234762967-234763946	K562	blood:	n/a	chr2:234763473-234763491
37	TCF12	chr2:234762831-234763771	ECC-1	luminal epithelium:	n/a	n/a
38	MAFK	chr2:234763308-234763854	HepG2	liver:	n/a	chr2:234763695-234763710 chr2:234763415-234763429
39	E2F6	chr2:234762867-234763869	A549	lung:	n/a	chr2:234763462-234763473
40	BCL3	chr2:234762932-234764174	A549	lung:	n/a	chr2:234763009-234763022
41	CREB1	chr2:234762771-234763773	HepG2	liver:	n/a	n/a
42	SIN3AK20	chr2:234762986-234763983	A549	lung:	n/a	n/a
43	MYBL2	chr2:234762860-234763777	HepG2	liver:	n/a	n/a
44	NFYB	chr2:234762982-234763836	GM12878	blood:	n/a	chr2:234763274-234763289
45	POLR2A	chr2:234761989-234763791	SK-N-MC	brain:	n/a	n/a
46	MAZ	chr2:234763037-234763779	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:234762817-234764386	PANC-1	pancreas:	n/a	n/a
48	TAF1	chr2:234762630-234763768	A549	lung:	n/a	n/a
49	POLR2A	chr2:234762783-234763790	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr2:234761676-234764238	Hela-S3	cervix:	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	chr2:234762991..234763952-chr6:26043968..26044562,2	Hela-S3	cervix:
4	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:
5	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:
6	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:
7	chr2:233739634..233741752-chr2:234762062..234763820,2	MCF-7	breast:

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000234816	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000201013	Chromatin interaction
ENSG00000182600	Chromatin interaction
ENSG00000144481	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12692249	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169922	0.97[ASN][1000 genomes]
rs169925	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]
rs183331	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs213545	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2286433	1.00[CEU][hapmap]
rs2302156	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4663339	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs501145	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs503913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs525359	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs528971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531643	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554699	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556691	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs580045	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs619929	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs626110	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs637082	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs638071	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6431643	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6431644	0.97[ASN][1000 genomes]
rs648818	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]
rs650570	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs650700	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs654279	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689101	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570755	0.92[CEU][hapmap]
rs887062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234761200-234764000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:234761400-234763800	Active TSS	NHDF-Ad	bronchial
3	chr2:234761400-234764000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr2:234761600-234763800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:234761600-234763800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:234761600-234763800	Active TSS	Fetal Kidney	kidney
7	chr2:234761600-234763800	Active TSS	GM12878-XiMat	blood
8	chr2:234761800-234763800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:234761800-234763800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:234761800-234763800	Active TSS	Fetal Intestine Small	intestine
11	chr2:234761800-234763800	Active TSS	Rectal Smooth Muscle	rectum
12	chr2:234761800-234764000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:234761800-234764000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:234762000-234763800	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr2:234762000-234763800	Active TSS	Fetal Intestine Large	intestine
16	chr2:234762000-234763800	Active TSS	HSMM	muscle
17	chr2:234762000-234764000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:234762000-234764000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr2:234762200-234763800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:234762200-234763800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:234762200-234763800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:234762200-234764000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr2:234762200-234764000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr2:234762400-234763800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:234762400-234763800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:234762400-234763800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:234762400-234763800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr2:234762400-234763800	Active TSS	Brain Substantia Nigra	brain
29	chr2:234762400-234763800	Active TSS	HSMMtube	muscle
30	chr2:234762400-234764200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr2:234762400-234764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:234762600-234763800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:234762600-234763800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:234762600-234763800	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr2:234762600-234763800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:234762600-234763800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:234762600-234763800	Active TSS	Brain Angular Gyrus	brain
38	chr2:234762600-234763800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr2:234762600-234763800	Active TSS	Placenta Amnion	Placenta Amnion
40	chr2:234762600-234763800	Active TSS	Psoas Muscle	Psoas
41	chr2:234762600-234763800	Active TSS	Right Atrium	heart
42	chr2:234762600-234763800	Active TSS	A549	lung
43	chr2:234762600-234763800	Active TSS	NH-A	brain
44	chr2:234762600-234764000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:234762800-234763800	Active TSS	Primary T cells from cord blood	blood
46	chr2:234762800-234763800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr2:234762800-234763800	Active TSS	Aorta	Aorta
48	chr2:234762800-234763800	Active TSS	Colon Smooth Muscle	Colon
49	chr2:234762800-234763800	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr2:234762800-234763800	Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links