Variant report

Variant	rs12621558
Chromosome Location	chr2:97490675-97490676
allele	C/T
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	chr2:97490674-97490730	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:97490254-97490739	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:97490357-97490687	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:97490376-97490701	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97426560..97429669-chr2:97487357..97491316,3	MCF-7	breast:
2	chr2:97488123..97491381-chr2:97522097..97525123,6	MCF-7	breast:
3	chr2:97489114..97491853-chr2:97492088..97494709,3	K562	blood:

Variant related genes	Relation type
CNNM3	TF binding region
ENSG00000168763	Chromatin interaction
ENSG00000213337	Chromatin interaction
ENSG00000158158	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12612567	1.00[CEU][hapmap]
rs12615663	1.00[CEU][hapmap]
rs13421281	1.00[CEU][hapmap]
rs57666657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61173747	1.00[AMR][1000 genomes]
rs61661673	1.00[EUR][1000 genomes];0.97[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	chr2:97483000-97490800	Enhancers	Fetal Heart	heart
2	chr2:97483600-97492200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:97483600-97493400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:97483600-97493400	Weak transcription	HSMMtube	muscle
5	chr2:97483600-97498200	Weak transcription	HSMM	muscle
6	chr2:97483800-97492200	Weak transcription	NHLF	lung
7	chr2:97483800-97493200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:97483800-97493400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:97483800-97493600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:97483800-97494400	Weak transcription	Osteobl	bone
11	chr2:97483800-97498400	Weak transcription	NHDF-Ad	bronchial
12	chr2:97484000-97493200	Weak transcription	Fetal Kidney	kidney
13	chr2:97484000-97493600	Weak transcription	NHEK	skin
14	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
15	chr2:97484800-97493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:97485200-97490800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:97485200-97490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:97485200-97498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:97485600-97493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
21	chr2:97486600-97490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:97486600-97491600	Weak transcription	Primary B cells from cord blood	blood
23	chr2:97486600-97492200	Weak transcription	K562	blood
24	chr2:97486600-97492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:97486600-97498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:97486800-97490800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
28	chr2:97487000-97498800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:97487200-97490800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:97487200-97491200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
32	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:97487400-97499200	Weak transcription	Fetal Brain Male	brain
34	chr2:97487400-97501800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:97487400-97504200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:97487600-97491000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:97487600-97491800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:97487600-97492000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:97487600-97492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:97487600-97493400	Weak transcription	Small Intestine	intestine
41	chr2:97487600-97493800	Weak transcription	GM12878-XiMat	blood
42	chr2:97487600-97504600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:97488000-97497400	Strong transcription	Spleen	Spleen
44	chr2:97488000-97498200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:97488000-97499000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:97488000-97501200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:97488200-97491000	Genic enhancers	Pancreas	Pancrea
48	chr2:97488200-97497000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:97488200-97497400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:97488200-97497400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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