Variant report

Variant	rs2276654
Chromosome Location	chr2:97492479-97492480
allele	A/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	POLR2A	chr2:97492286-97492987	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:97491961-97492772	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:97492452-97492679	ProgFib	skin:	n/a	n/a
4	POLR2A	chr2:97492195-97492754	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97492185..97494409-chr2:97534790..97536451,2	MCF-7	breast:
2	chr2:97489114..97491853-chr2:97492088..97494709,3	K562	blood:

Variant related genes	Relation type
CNNM3	TF binding region
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10203346	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10439526	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11889085	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11897786	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12172	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12846	0.80[EUR][1000 genomes]
rs1317911	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs1320146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320149	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs13419073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs17119564	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs17119591	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17119598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139406	1.00[GIH][hapmap]
rs2280356	1.00[GIH][hapmap]
rs2314399	0.83[ASN][1000 genomes]
rs2872633	1.00[GIH][hapmap]
rs3731940	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs3731941	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4077343	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56797569	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56913233	0.83[ASN][1000 genomes]
rs57582887	0.83[ASN][1000 genomes]
rs58147284	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59244622	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152765	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152766	0.83[ASN][1000 genomes]
rs62152767	0.83[ASN][1000 genomes]
rs62152768	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152770	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152771	0.83[ASN][1000 genomes]
rs62152772	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152773	0.83[ASN][1000 genomes]
rs62152774	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152775	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152777	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62152783	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62152784	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62152785	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62152786	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62152787	0.88[ASN][1000 genomes]
rs62152788	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62152790	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152793	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152794	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152795	0.84[EUR][1000 genomes]
rs62152834	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152860	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62152863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152864	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62156208	0.83[ASN][1000 genomes]
rs62156209	0.83[ASN][1000 genomes]
rs62156210	0.83[ASN][1000 genomes]
rs62156211	0.83[ASN][1000 genomes]
rs62156212	0.83[ASN][1000 genomes]
rs62156213	0.83[ASN][1000 genomes]
rs62156216	0.83[ASN][1000 genomes]
rs62156219	0.83[ASN][1000 genomes]
rs62156220	0.83[ASN][1000 genomes]
rs62156221	0.83[ASN][1000 genomes]
rs62156222	0.83[ASN][1000 genomes]
rs62156223	0.83[ASN][1000 genomes]
rs62156225	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156226	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156227	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156228	0.83[ASN][1000 genomes]
rs62156230	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156231	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156232	0.83[ASN][1000 genomes]
rs62156233	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62156234	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6576981	0.83[ASN][1000 genomes]
rs6576986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576989	0.88[MEX][hapmap]
rs6751132	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs6753987	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs6756482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758151	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs72809850	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72811623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811627	1.00[AMR][1000 genomes]
rs72811629	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7568206	0.83[ASN][1000 genomes]
rs7580942	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7594727	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7608621	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs878064	0.81[ASN][1000 genomes]
rs9948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs9973492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 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	chr2:97483600-97493400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:97483600-97493400	Weak transcription	HSMMtube	muscle
3	chr2:97483600-97498200	Weak transcription	HSMM	muscle
4	chr2:97483800-97493200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:97483800-97493400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:97483800-97493600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:97483800-97494400	Weak transcription	Osteobl	bone
8	chr2:97483800-97498400	Weak transcription	NHDF-Ad	bronchial
9	chr2:97484000-97493200	Weak transcription	Fetal Kidney	kidney
10	chr2:97484000-97493600	Weak transcription	NHEK	skin
11	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
12	chr2:97484800-97493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:97485200-97498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:97485600-97493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
16	chr2:97486600-97492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:97486600-97498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
19	chr2:97487000-97498800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
21	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:97487400-97499200	Weak transcription	Fetal Brain Male	brain
23	chr2:97487400-97501800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:97487400-97504200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:97487600-97492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:97487600-97493400	Weak transcription	Small Intestine	intestine
27	chr2:97487600-97493800	Weak transcription	GM12878-XiMat	blood
28	chr2:97487600-97504600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:97488000-97497400	Strong transcription	Spleen	Spleen
30	chr2:97488000-97498200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:97488000-97499000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:97488000-97501200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:97488200-97497000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:97488200-97497400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:97488200-97497400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:97488200-97497400	Strong transcription	Placenta	Placenta
37	chr2:97488200-97497600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:97488200-97497600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:97488200-97499200	Strong transcription	Brain Germinal Matrix	brain
40	chr2:97488200-97499600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:97488200-97501200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:97488200-97501800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:97488400-97497800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:97488400-97499200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:97488400-97499400	Strong transcription	Brain Substantia Nigra	brain
46	chr2:97488400-97499600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:97488400-97501200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:97488600-97497400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:97488600-97497800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:97488600-97497800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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