Variant report

Variant	rs4765830
Chromosome Location	chr12:1721254-1721255
allele	G/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	MAX	chr12:1720973-1721256	NB4	blood:	n/a	n/a
2	FOSL2	chr12:1720835-1721492	SK-N-SH	brain:	n/a	n/a
3	MAX	chr12:1720940-1721302	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:1720849-1721432	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr12:1720886-1721545	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr12:1720619-1722028	IMR90	lung:	n/a	n/a
7	GATA3	chr12:1720805-1721415	SK-N-SH	brain:	n/a	n/a
8	MYC	chr12:1720953-1721340	NB4	blood:	n/a	n/a
9	MAFK	chr12:1720974-1721328	IMR90	lung:	n/a	chr12:1720999-1721010 chr12:1720999-1721015
10	TCF12	chr12:1720700-1721523	SK-N-SH	brain:	n/a	n/a
11	EP300	chr12:1720948-1721307	SK-N-SH_RA	brain:	n/a	chr12:1721067-1721081
12	TCF12	chr12:1720677-1721587	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr12:1720982-1721289	SK-N-SH	brain:	n/a	n/a
14	EP300	chr12:1720958-1721307	SK-N-SH_RA	brain:	n/a	chr12:1721067-1721081
15	EP300	chr12:1720777-1721544	SK-N-SH	brain:	n/a	chr12:1721067-1721081
16	CEBPB	chr12:1720874-1721299	IMR90	lung:	n/a	chr12:1721068-1721079
17	RXRA	chr12:1720866-1721420	SK-N-SH	brain:	n/a	chr12:1720923-1720932
18	PBX3	chr12:1720796-1721456	SK-N-SH	brain:	n/a	n/a
19	JUND	chr12:1720778-1721456	SK-N-SH	brain:	n/a	n/a
20	PBX3	chr12:1720866-1721416	SK-N-SH	brain:	n/a	n/a
21	FOS	chr12:1721046-1721329	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1716647..1719370-chr12:1719904..1722064,2	MCF-7	breast:
2	chr12:1713181..1716889-chr12:1718186..1722611,7	K562	blood:

Variant related genes	Relation type
WNT5B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2003510	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765829	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4765831	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7314822	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316135	0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs740355	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv898586	chr12:1690140-1734365	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv1834423	chr12:1703324-1727170	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4765830	WNT5B	cis	multi-tissue	Pritchard
rs4765830	FGF23	cis	cerebellum	SCAN
rs4765830	SLC6A12	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1715200-1723600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:1715200-1725800	Weak transcription	Esophagus	oesophagus
3	chr12:1715400-1721800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:1715400-1738600	Weak transcription	Right Atrium	heart
5	chr12:1715600-1721600	Enhancers	Liver	Liver
6	chr12:1716200-1734600	Weak transcription	Fetal Stomach	stomach
7	chr12:1717000-1728800	Weak transcription	Lung	lung
8	chr12:1717600-1723000	Weak transcription	K562	blood
9	chr12:1717800-1723600	Weak transcription	Primary B cells from cord blood	blood
10	chr12:1718200-1725200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:1718400-1722200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:1719600-1721600	Weak transcription	Ovary	ovary
13	chr12:1719600-1725600	Weak transcription	Thymus	Thymus
14	chr12:1719600-1728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:1720000-1725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:1720200-1727200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:1720200-1727200	Weak transcription	Stomach Mucosa	stomach
18	chr12:1720600-1721400	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr12:1720600-1721400	Enhancers	Fetal Muscle Trunk	muscle
20	chr12:1720600-1721600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:1720600-1721600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:1720600-1721600	Enhancers	Adipose Nuclei	Adipose
23	chr12:1720600-1721600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr12:1720600-1721600	Enhancers	Fetal Lung	lung
25	chr12:1720600-1721600	Enhancers	Fetal Muscle Leg	muscle
26	chr12:1720600-1721600	Enhancers	HMEC	breast
27	chr12:1720600-1721600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr12:1720600-1721800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:1720600-1721800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:1720600-1721800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:1720600-1721800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:1720600-1722000	Enhancers	Brain Germinal Matrix	brain
33	chr12:1720800-1721400	Enhancers	Colon Smooth Muscle	Colon
34	chr12:1720800-1721400	Active TSS	Stomach Smooth Muscle	stomach
35	chr12:1720800-1721600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:1720800-1721600	Bivalent Enhancer	HepG2	liver
37	chr12:1720800-1721600	Flanking Active TSS	Osteobl	bone
38	chr12:1720800-1722000	Enhancers	Fetal Brain Male	brain
39	chr12:1720800-1722200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:1720800-1725600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:1721000-1721400	Enhancers	Brain Angular Gyrus	brain
42	chr12:1721000-1721600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:1721000-1721600	Enhancers	Brain Cingulate Gyrus	brain
44	chr12:1721000-1721800	Enhancers	Fetal Brain Female	brain
45	chr12:1721000-1734400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:1721200-1721400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:1721200-1721400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr12:1721200-1721400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr12:1721200-1721400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:1721200-1721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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