Variant report

Variant	rs2728669
Chromosome Location	chr12:32590651-32590652
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	chr12:32590578..32592107-chr12:32597792..32599850,2	MCF-7	breast:
2	chr12:32588671..32590721-chr12:32830840..32833559,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087470	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10844200	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844201	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1500874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809912	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1809913	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2062602	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2088806	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088807	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2243815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389035	0.98[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2389036	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2467065	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470382	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2651360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2651361	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2651362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2651363	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651369	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2651378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2651379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2728671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728673	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2728674	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2728680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2728682	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2728683	0.91[AFR][1000 genomes]
rs2728684	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2728713	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2733682	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs325417	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7296118	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs904917	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs950079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950081	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs950082	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv469347	chr12:32555846-32602079	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv558189	chr12:32555846-32602079	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:32573400-32593400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:32580400-32593200	Weak transcription	Fetal Intestine Large	intestine
4	chr12:32582600-32591000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:32582600-32593600	Weak transcription	Fetal Stomach	stomach
6	chr12:32582600-32598600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:32584200-32591200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:32587400-32591400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:32587400-32591400	Enhancers	HUVEC	blood vessel
10	chr12:32588200-32591400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:32588600-32591000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:32588600-32591200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:32588600-32591200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr12:32588800-32590800	Enhancers	NH-A	brain
15	chr12:32588800-32591000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:32588800-32591000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:32588800-32591000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:32588800-32591000	Enhancers	HepG2	liver
19	chr12:32588800-32591200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:32588800-32591200	Enhancers	NHEK	skin
21	chr12:32588800-32591400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:32589000-32591000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:32589000-32591400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr12:32589000-32593400	Enhancers	HMEC	breast
25	chr12:32589200-32591200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:32589400-32591000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:32589400-32591000	Enhancers	HSMM	muscle
28	chr12:32589400-32598400	Weak transcription	Brain Substantia Nigra	brain
29	chr12:32589600-32592400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:32589600-32597400	Weak transcription	Stomach Mucosa	stomach
31	chr12:32589800-32591000	Enhancers	Lung	lung
32	chr12:32590000-32590800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:32590200-32597800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:32590400-32590800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr12:32590400-32591800	Strong transcription	Fetal Intestine Small	intestine
36	chr12:32590400-32593400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32590400-32593400	Weak transcription	Left Ventricle	heart
38	chr12:32590400-32593800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:32590600-32590800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:32590600-32591000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:32590600-32591200	Enhancers	Hela-S3	cervix
42	chr12:32590600-32591400	Enhancers	A549	lung
43	chr12:32590600-32591800	Enhancers	Placenta	Placenta
44	chr12:32590600-32592400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:32590600-32593200	Weak transcription	Ovary	ovary
46	chr12:32590600-32593800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links