Variant report

Variant	rs4765829
Chromosome Location	chr12:1720794-1720795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1716647..1719370-chr12:1719904..1722064,2	MCF-7	breast:
2	chr12:1699199..1708657-chr12:1712989..1721243,16	MCF-7	breast:
3	chr12:1713181..1716889-chr12:1718186..1722611,7	K562	blood:

Variant related genes	Relation type
ENSG00000171823	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2003510	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765830	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]
rs4766395	0.90[JPT][hapmap]
rs7308793	0.90[JPT][hapmap]
rs7314822	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316135	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs740355	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4765829	SLC6A12	cis	parietal	SCAN
rs4765829	FGF23	cis	cerebellum	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	chr12:1715600-1720800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:1715600-1720800	Weak transcription	Fetal Brain Male	brain
7	chr12:1715600-1721000	Weak transcription	Fetal Brain Female	brain
8	chr12:1715600-1721200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:1715600-1721600	Enhancers	Liver	Liver
10	chr12:1715800-1721000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:1715800-1721000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:1716200-1720800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:1716200-1720800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:1716200-1721200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:1716200-1721200	Weak transcription	Fetal Heart	heart
16	chr12:1716200-1734600	Weak transcription	Fetal Stomach	stomach
17	chr12:1717000-1728800	Weak transcription	Lung	lung
18	chr12:1717600-1721200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:1717600-1723000	Weak transcription	K562	blood
20	chr12:1717800-1720800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:1717800-1723600	Weak transcription	Primary B cells from cord blood	blood
22	chr12:1718000-1720800	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:1718000-1720800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:1718200-1721000	Weak transcription	HSMMtube	muscle
25	chr12:1718200-1725200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:1718400-1722200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:1719400-1720800	Enhancers	Osteobl	bone
28	chr12:1719600-1721600	Weak transcription	Ovary	ovary
29	chr12:1719600-1725600	Weak transcription	Thymus	Thymus
30	chr12:1719600-1728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:1720000-1720800	Enhancers	HepG2	liver
32	chr12:1720000-1725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:1720200-1727200	Weak transcription	Fetal Intestine Small	intestine
34	chr12:1720200-1727200	Weak transcription	Stomach Mucosa	stomach
35	chr12:1720400-1720800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:1720400-1721200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:1720400-1721200	Enhancers	NHLF	lung
38	chr12:1720600-1720800	Enhancers	Stomach Smooth Muscle	stomach
39	chr12:1720600-1720800	Flanking Active TSS	HSMM	muscle
40	chr12:1720600-1721000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:1720600-1721000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:1720600-1721000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr12:1720600-1721000	Flanking Active TSS	NHDF-Ad	bronchial
44	chr12:1720600-1721200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:1720600-1721200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr12:1720600-1721200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:1720600-1721200	Enhancers	NH-A	brain
48	chr12:1720600-1721400	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr12:1720600-1721400	Enhancers	Fetal Muscle Trunk	muscle
50	chr12:1720600-1721600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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