Variant report

Variant	rs12988261
Chromosome Location	chr2:64365909-64365910
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	CTCF	chr2:64365780-64365930	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr2:64365071-64366189	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:64364848..64367647-chr2:64381167..64383124,2	K562	blood:
2	chr2:64365394..64367023-chr2:64370250..64372565,2	MCF-7	breast:
3	chr2:64360272..64363388-chr2:64364975..64368007,3	MCF-7	breast:
4	chr2:64364705..64366411-chr2:64549712..64552538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225889	TF binding region
ENSG00000225889	Chromatin interaction
ENSG00000197329	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12472736	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12472816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12477310	0.83[ASN][1000 genomes]
rs12479211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34283299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67361634	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7349403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64340400-64370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:64347400-64368800	Weak transcription	Spleen	Spleen
3	chr2:64348400-64366400	Weak transcription	Right Atrium	heart
4	chr2:64355400-64368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:64356200-64368600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:64356400-64368200	Weak transcription	Brain Germinal Matrix	brain
7	chr2:64356400-64368800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:64357200-64367000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:64357200-64368200	Weak transcription	Liver	Liver
10	chr2:64357200-64369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:64357800-64366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:64357800-64367000	Weak transcription	HepG2	liver
13	chr2:64359000-64368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:64359000-64368800	Weak transcription	Right Ventricle	heart
15	chr2:64359200-64366200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:64359400-64368600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:64360000-64366800	Enhancers	NHDF-Ad	bronchial
18	chr2:64360600-64368800	Weak transcription	Fetal Stomach	stomach
19	chr2:64361400-64368800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:64361800-64370000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:64362000-64366800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:64362200-64368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:64362400-64366800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:64362400-64368000	Weak transcription	Fetal Lung	lung
25	chr2:64362400-64368800	Weak transcription	NH-A	brain
26	chr2:64362600-64366800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:64362600-64367000	Weak transcription	Osteobl	bone
28	chr2:64362600-64368600	Enhancers	Primary T cells from cord blood	blood
29	chr2:64362600-64370000	Weak transcription	Ovary	ovary
30	chr2:64362800-64367400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:64363000-64366600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:64363200-64367000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:64363200-64368800	Enhancers	Brain Substantia Nigra	brain
34	chr2:64363200-64368800	Enhancers	Colon Smooth Muscle	Colon
35	chr2:64363400-64367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:64363400-64368200	Weak transcription	Dnd41	blood
37	chr2:64363600-64366600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:64363600-64367000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:64363600-64368000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:64363800-64367400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:64364000-64366000	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:64364000-64366200	Enhancers	Brain Angular Gyrus	brain
43	chr2:64364000-64366800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:64364000-64368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:64364000-64370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:64364000-64370400	Weak transcription	Lung	lung
47	chr2:64364200-64366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:64364400-64366000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr2:64364400-64366000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:64364400-64366000	Enhancers	K562	blood

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