Variant report

Variant	rs2240514
Chromosome Location	chr12:1753855-1753856
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	GATA2	chr12:1753012-1754336	SH-SY5Y	brain:	n/a	n/a
2	NFIC	chr12:1753499-1754155	SK-N-SH	brain:	n/a	n/a
3	MYC	chr12:1753760-1754008	MCF10A-Er-Src	breast:	n/a	chr12:1753890-1753899
4	YY1	chr12:1753704-1754044	SK-N-SH_RA	brain:	n/a	chr12:1753854-1753862
5	POLR2A	chr12:1753625-1754199	H1-neurons	neurons:	n/a	n/a
6	FOS	chr12:1753805-1753959	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:1753669-1754104	H1-neurons	neurons:	n/a	n/a
8	MAX	chr12:1753643-1754148	SK-N-SH	brain:	n/a	chr12:1753890-1753899
9	TCF12	chr12:1753470-1754237	SK-N-SH	brain:	n/a	n/a
10	EP300	chr12:1753683-1753946	SK-N-SH_RA	brain:	n/a	n/a
11	MAFK	chr12:1753742-1754084	IMR90	lung:	n/a	n/a
12	MXI1	chr12:1753495-1754302	IMR90	lung:	n/a	n/a
13	MXI1	chr12:1753051-1754439	SK-N-SH	brain:	n/a	n/a
14	EP300	chr12:1753704-1754040	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
WNT5B	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11061892	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240508	0.91[ASN][1000 genomes]
rs2240509	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240511	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240512	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240513	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2369972	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3803164	0.87[ASN][1000 genomes]
rs735890	0.93[ASN][1000 genomes]
rs735891	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv898587	chr12:1732295-1756642	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv898588	chr12:1736314-1755960	Bivalent Enhancer Enhancers Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv898589	chr12:1738111-1755654	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv898590	chr12:1740171-1757743	Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv898591	chr12:1745208-1755960	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv468964	chr12:1749905-1769930	Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv556995	chr12:1749905-1769930	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1740600-1755000	Weak transcription	Spleen	Spleen
2	chr12:1740800-1757400	Weak transcription	GM12878-XiMat	blood
3	chr12:1743600-1759000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:1744400-1759000	Weak transcription	Right Ventricle	heart
5	chr12:1744600-1758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:1746600-1758000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:1747800-1754600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:1747800-1755800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:1747800-1756000	Weak transcription	K562	blood
10	chr12:1749200-1760200	Weak transcription	Gastric	stomach
11	chr12:1750000-1754800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:1750000-1766800	Weak transcription	Pancreas	Pancrea
13	chr12:1750600-1754800	Weak transcription	Thymus	Thymus
14	chr12:1751000-1755000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:1751800-1754000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:1752000-1754000	Weak transcription	Fetal Intestine Small	intestine
17	chr12:1752000-1754800	Enhancers	Fetal Stomach	stomach
18	chr12:1752000-1769400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:1752400-1755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:1752400-1755200	Enhancers	Fetal Heart	heart
21	chr12:1752400-1755600	Weak transcription	Fetal Intestine Large	intestine
22	chr12:1753000-1754200	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:1753000-1754400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:1753000-1754400	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:1753000-1754400	Enhancers	Fetal Muscle Leg	muscle
26	chr12:1753000-1754400	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr12:1753000-1754600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr12:1753000-1754600	Enhancers	Fetal Lung	lung
29	chr12:1753200-1754000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:1753200-1754000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:1753200-1754000	Enhancers	NHDF-Ad	bronchial
32	chr12:1753200-1754200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:1753200-1754200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:1753200-1754200	Enhancers	Colonic Mucosa	Colon
35	chr12:1753200-1754200	Enhancers	Left Ventricle	heart
36	chr12:1753200-1754400	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr12:1753200-1754400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:1753200-1754400	Enhancers	Duodenum Mucosa	Duodenum
39	chr12:1753200-1754400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr12:1753200-1754400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:1753200-1754400	Enhancers	NH-A	brain
42	chr12:1753200-1754600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:1753200-1754600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:1753200-1754600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:1753200-1754600	Enhancers	Fetal Muscle Trunk	muscle
46	chr12:1753200-1754600	Genic enhancers	NHLF	lung
47	chr12:1753200-1757000	Enhancers	Fetal Thymus	thymus
48	chr12:1753400-1754000	Weak transcription	Right Atrium	heart
49	chr12:1753400-1754200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:1753400-1754200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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