Variant report

Variant	rs2307059
Chromosome Location	chr12:46781634-46781635
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:13)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr12:46780274-46782562	GM19099	blood:	n/a	n/a
2	RELA	chr12:46780469-46781812	GM19193	blood:	n/a	n/a
3	PML	chr12:46780131-46781875	GM12878	blood:	n/a	n/a
4	EP300	chr12:46781506-46783301	GM12878	blood:	n/a	chr12:46782338-46782347 chr12:46782337-46782351 chr12:46782418-46782432
5	MTA3	chr12:46781457-46782698	GM12878	blood:	n/a	n/a
6	RELA	chr12:46780650-46781923	GM15510	blood:	n/a	n/a
7	POLR2A	chr12:46781541-46781691	Gliobla	brain:	n/a	n/a
8	MYC	chr12:46781549-46781804	NB4	blood:	n/a	n/a
9	FOXM1	chr12:46780638-46781799	GM12878	blood:	n/a	n/a
10	TBP	chr12:46781297-46781912	GM12878	blood:	n/a	n/a
11	PAX5	chr12:46781462-46781764	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:46781557-46781680	ProgFib	skin:	n/a	n/a
13	STAT1	chr12:46781606-46781806	GM12878	blood:	n/a	n/a
14	MTA3	chr12:46781300-46782676	GM12878	blood:	n/a	n/a
15	IRF4	chr12:46781487-46781961	GM12878	blood:	n/a	n/a
16	EBF1	chr12:46781431-46781788	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:46780119-46782654	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:46780098-46783057	GM12891	blood:	n/a	n/a
19	WRNIP1	chr12:46781544-46781975	GM12878	blood:	n/a	n/a
20	EBF1	chr12:46781400-46781855	GM12878	blood:	n/a	n/a
21	TFAP2C	chr12:46780733-46781763	Hela-S3	cervix:	n/a	chr12:46781247-46781262
22	BATF	chr12:46781488-46781841	GM12878	blood:	n/a	n/a
23	RELA	chr12:46780380-46781866	GM12878	blood:	n/a	n/a
24	SMARCC1	chr12:46780297-46781874	Hela-S3	cervix:	n/a	n/a
25	RELA	chr12:46780650-46781960	GM18951	blood:	n/a	n/a
26	RUNX3	chr12:46781327-46783021	GM12878	blood:	n/a	n/a
27	EBF1	chr12:46781315-46782627	GM12878	blood:	n/a	n/a
28	RELA	chr12:46780653-46781895	GM12891	blood:	n/a	n/a
29	CREB1	chr12:46780304-46782638	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:46780681-46781677	SK-N-MC	brain:	n/a	n/a
31	SMC3	chr12:46781312-46782499	GM12878	blood:	n/a	n/a
32	MAX	chr12:46780776-46781846	GM12878	blood:	n/a	n/a
33	ZNF143	chr12:46781494-46781895	GM12878	blood:	n/a	n/a
34	RUNX3	chr12:46781390-46781978	GM12878	blood:	n/a	n/a
35	IKZF1	chr12:46780744-46781698	GM12878	blood:	n/a	n/a
36	TCF7L2	chr12:46780102-46781741	Hela-S3	cervix:	n/a	n/a
37	BHLHE40	chr12:46780432-46781821	GM12878	blood:	n/a	chr12:46781195-46781216
38	TFAP2A	chr12:46780817-46781664	Hela-S3	cervix:	n/a	chr12:46781245-46781260
39	NFIC	chr12:46779940-46783129	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46781039..46783581-chr12:46796813..46799166,3	K562	blood:
2	chr12:46781028..46783722-chr12:46834423..46837382,2	K562	blood:

(count:13 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-3	chr12:46781530-46781755	XLOC_009723
2	lnc-ARID2-3	chr12:46781630-46781755	XLOC_009723
3	lnc-ARID2-3	chr12:46781530-46781755	XLOC_009723
4	lnc-ARID2-3	chr12:46781530-46781934	XLOC_009723
5	lnc-ARID2-3	chr12:46781530-46781755	XLOC_009723
6	lnc-ARID2-3	chr12:46781530-46781755	XLOC_009723
7	lnc-ARID2-3	chr12:46781530-46781755	ENSG00000257261.1
8	lnc-ARID2-3	chr12:46781530-46781755	ENSG00000257261.1
9	lnc-ARID2-3	chr12:46781530-46781755	NONHSAT027872
10	lnc-ARID2-3	chr12:46781530-46781755	NONHSAT027868
11	lnc-ARID2-3	chr12:46781530-46781755	NONHSAT027865
12	lnc-ARID2-3	chr12:46781530-46781757	NONHSAT027867
13	lnc-ARID2-3	chr12:46781530-46781755	NONHSAT027871

No data

Variant related genes	Relation type
ENSG00000257496	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11183453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183454	0.85[JPT][hapmap]
rs1125908	0.94[JPT][hapmap]
rs11833812	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834593	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17096884	0.89[JPT][hapmap]
rs1948425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125646	0.84[JPT][hapmap]
rs2307062	0.84[JPT][hapmap]
rs2307063	0.81[CHB][hapmap]
rs2408509	0.84[JPT][hapmap]
rs3742061	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs55795804	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57199226	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57786829	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58545634	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59546893	0.94[EUR][1000 genomes]
rs73282593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967840	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' 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	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46778200-46784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:46778400-46782200	Enhancers	Colon Smooth Muscle	Colon
3	chr12:46778400-46782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:46778400-46782800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:46778400-46783400	Enhancers	Fetal Heart	heart
6	chr12:46778400-46784200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:46778400-46786800	Enhancers	NHDF-Ad	bronchial
8	chr12:46778600-46781800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:46778600-46782000	Enhancers	Fetal Kidney	kidney
10	chr12:46778600-46782400	Enhancers	Dnd41	blood
11	chr12:46778600-46783600	Enhancers	HMEC	breast
12	chr12:46778600-46784200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:46778600-46785400	Enhancers	Adipose Nuclei	Adipose
14	chr12:46778600-46787000	Enhancers	Fetal Lung	lung
15	chr12:46778800-46784000	Enhancers	Duodenum Mucosa	Duodenum
16	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:46779200-46783400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:46779400-46782000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:46779400-46782800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:46779600-46782800	Weak transcription	Ovary	ovary
21	chr12:46779600-46783600	Enhancers	NH-A	brain
22	chr12:46779600-46786000	Weak transcription	Gastric	stomach
23	chr12:46779600-46786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:46779600-46786400	Weak transcription	Right Ventricle	heart
25	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
26	chr12:46780000-46782200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr12:46780200-46782400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:46780400-46782200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:46780400-46782200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:46780400-46783200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr12:46780400-46784400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:46780600-46782000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:46780600-46782200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:46780600-46782800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:46780600-46783200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr12:46780600-46783200	Enhancers	Fetal Thymus	thymus
37	chr12:46780600-46783400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr12:46780600-46786800	Weak transcription	Brain Substantia Nigra	brain
39	chr12:46780600-46788600	Weak transcription	Fetal Brain Male	brain
40	chr12:46780800-46781800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr12:46780800-46781800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:46780800-46781800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:46780800-46781800	Enhancers	Fetal Muscle Trunk	muscle
44	chr12:46780800-46781800	Enhancers	Fetal Muscle Leg	muscle
45	chr12:46780800-46781800	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:46780800-46782000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:46780800-46782000	Enhancers	Placenta	Placenta
48	chr12:46780800-46782000	Enhancers	Psoas Muscle	Psoas
49	chr12:46780800-46782400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:46780800-46783000	Enhancers	Thymus	Thymus

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