Variant report

Variant	rs12462674
Chromosome Location	chr19:36571802-36571803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36565855..36568123-chr19:36571132..36573817,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1003470	0.87[YRI][hapmap]
rs10407011	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10414877	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10420353	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10421966	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10423651	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10425692	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426582	0.81[CHB][hapmap]
rs12462432	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462632	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972490	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12976505	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12976812	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12977802	0.84[JPT][hapmap]
rs12977814	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978482	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12981654	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1548505	0.87[YRI][hapmap]
rs17639286	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2023865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072606	0.89[JPT][hapmap]
rs2079151	0.82[ASN][1000 genomes]
rs2239510	0.96[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2301736	0.87[YRI][hapmap]
rs2311004	0.82[YRI][hapmap]
rs35125548	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35875194	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3826995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4461192	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4805154	0.81[CHB][hapmap]
rs4806280	0.84[JPT][hapmap]
rs56034793	0.90[ASN][1000 genomes]
rs62109743	0.90[ASN][1000 genomes]
rs71337524	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs721542	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245762	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7246292	0.87[YRI][hapmap]
rs7250448	0.85[CHB][hapmap]
rs7257383	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7259592	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7260609	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36572400	Weak transcription	Lung	lung
4	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
5	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
10	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
14	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:36552000-36572400	Weak transcription	Liver	Liver
16	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
17	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
18	chr19:36558200-36572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:36558800-36574000	Weak transcription	Gastric	stomach
20	chr19:36559000-36572400	Weak transcription	Placenta	Placenta
21	chr19:36559200-36572600	Weak transcription	Fetal Brain Female	brain
22	chr19:36559200-36572800	Weak transcription	Brain Germinal Matrix	brain
23	chr19:36560400-36580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr19:36561000-36572200	Weak transcription	Fetal Intestine Large	intestine
25	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:36561200-36597600	Strong transcription	Dnd41	blood
29	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:36561600-36572000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:36561800-36572000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:36561800-36572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr19:36561800-36574200	Weak transcription	NH-A	brain
38	chr19:36562000-36572400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:36562000-36588600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:36562200-36585000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:36563000-36572600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:36563000-36594200	Weak transcription	HSMM	muscle
43	chr19:36563600-36572000	Weak transcription	Osteobl	bone
44	chr19:36564400-36574200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:36564800-36572000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:36564800-36572200	Weak transcription	NHEK	skin
47	chr19:36564800-36572200	Weak transcription	NHLF	lung
48	chr19:36564800-36572400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:36564800-36584600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:36565000-36572000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links