Variant report

Variant	rs2302685
Chromosome Location	chr12:12301898-12301899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12296863..12299099-chr12:12301647..12304445,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10466846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11054704	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11054741	0.80[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap]
rs1181332	0.80[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap]
rs12314349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12823867	0.80[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap]
rs2160525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2302685	PRH1	cis	parietal	SCAN
rs2302685	LRP6	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
3	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
7	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
8	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
11	chr12:12275000-12303400	Weak transcription	GM12878-XiMat	blood
12	chr12:12277400-12306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
15	chr12:12279800-12303600	Weak transcription	Fetal Brain Male	brain
16	chr12:12279800-12311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:12279800-12311000	Weak transcription	HMEC	breast
18	chr12:12279800-12311600	Weak transcription	Dnd41	blood
19	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:12280000-12302600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:12280000-12303400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
24	chr12:12283200-12303400	Weak transcription	HSMM	muscle
25	chr12:12283400-12309200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:12284800-12304600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:12285000-12309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:12285000-12311400	Weak transcription	Pancreas	Pancrea
29	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
30	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:12288200-12310600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:12288200-12342800	Weak transcription	K562	blood
33	chr12:12288600-12311400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:12292400-12304600	Strong transcription	Liver	Liver
36	chr12:12296400-12304000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:12297600-12321400	Weak transcription	Gastric	stomach
39	chr12:12298000-12306000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:12298000-12308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:12298800-12304000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:12298800-12304200	Strong transcription	Fetal Lung	lung
43	chr12:12298800-12304600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:12298800-12312200	Strong transcription	Fetal Intestine Large	intestine
45	chr12:12299000-12304000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:12299000-12304200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:12299000-12304200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:12299000-12304200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:12299000-12304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:12299000-12305800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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