Variant report

Variant	rs3803089
Chromosome Location	chr12:117383715-117383716
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	chr12:117174363..117175916-chr12:117381728..117384041,2	MCF-7	breast:
2	chr12:117383644..117386038-chr12:117390452..117392333,2	K562	blood:

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10507277	0.86[JPT][hapmap]
rs10732611	0.86[JPT][hapmap]
rs10735099	0.86[JPT][hapmap]
rs10744886	0.80[ASN][1000 genomes]
rs10774891	0.86[JPT][hapmap]
rs10774892	0.86[JPT][hapmap]
rs10774896	0.84[JPT][hapmap]
rs11068245	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11068247	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068258	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068280	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11068282	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068286	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068294	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11068296	0.84[JPT][hapmap]
rs11068310	0.91[JPT][hapmap]
rs17583145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17616662	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133684	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242469	0.93[JPT][hapmap]
rs2270792	0.92[JPT][hapmap]
rs2270793	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2291912	0.90[JPT][hapmap]
rs2393111	0.84[JPT][hapmap]
rs3782189	0.91[JPT][hapmap]
rs3782190	0.91[JPT][hapmap]
rs3893370	0.84[JPT][hapmap]
rs4074147	0.86[JPT][hapmap]
rs4076700	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs4077519	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4130296	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4299000	0.83[ASN][1000 genomes]
rs4347476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522274	0.86[JPT][hapmap]
rs4542506	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4562925	0.84[JPT][hapmap]
rs4766815	0.84[JPT][hapmap]
rs4766820	0.86[JPT][hapmap]
rs4766821	0.81[JPT][hapmap]
rs4767474	0.84[JPT][hapmap]
rs4767476	0.86[JPT][hapmap]
rs4767478	0.86[JPT][hapmap]
rs4767480	0.82[ASN][1000 genomes]
rs4767482	0.81[JPT][hapmap]
rs4767483	0.84[JPT][hapmap]
rs4767484	0.84[JPT][hapmap]
rs4767488	0.81[JPT][hapmap]
rs4767489	0.83[JPT][hapmap]
rs4767491	0.83[JPT][hapmap]
rs4767493	0.85[JPT][hapmap]
rs6490102	0.86[JPT][hapmap]
rs7131746	0.83[JPT][hapmap]
rs7136629	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7137006	0.85[JPT][hapmap]
rs7137752	0.84[JPT][hapmap]
rs7297446	0.90[JPT][hapmap]
rs7303882	0.86[JPT][hapmap]
rs7308498	0.86[JPT][hapmap]
rs7311972	0.84[JPT][hapmap]
rs7316144	0.85[JPT][hapmap]
rs7487081	0.84[JPT][hapmap]
rs7959666	0.86[JPT][hapmap]
rs7973240	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1046811	chr12:117353904-117396230	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	esv1798657	chr12:117354067-117392259	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1048942	chr12:117365506-117400588	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117358400-117392600	Weak transcription	Small Intestine	intestine
2	chr12:117363200-117399400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:117363400-117385000	Weak transcription	HUVEC	blood vessel
4	chr12:117365000-117406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:117365800-117383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:117366600-117388400	Weak transcription	K562	blood
7	chr12:117373800-117393200	Weak transcription	Stomach Mucosa	stomach
8	chr12:117374400-117385600	Weak transcription	NHDF-Ad	bronchial
9	chr12:117378000-117392600	Weak transcription	Psoas Muscle	Psoas
10	chr12:117381000-117385400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:117381200-117385200	Strong transcription	HSMM	muscle
12	chr12:117381200-117390200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:117381200-117391200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:117381400-117386000	Strong transcription	Aorta	Aorta
15	chr12:117381400-117387800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:117381400-117389600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:117381600-117384200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:117381600-117384600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:117381600-117386200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:117381600-117387200	Weak transcription	Fetal Brain Female	brain
21	chr12:117381600-117388000	Strong transcription	Fetal Intestine Large	intestine
22	chr12:117381600-117388600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:117381600-117390200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:117381600-117390400	Strong transcription	Primary T cells from cord blood	blood
25	chr12:117381600-117390800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:117381800-117384200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:117381800-117386200	Strong transcription	A549	lung
28	chr12:117381800-117387200	Weak transcription	HMEC	breast
29	chr12:117381800-117387800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:117381800-117387800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:117381800-117389200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:117381800-117390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:117381800-117390200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:117381800-117390400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:117381800-117391400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:117381800-117396200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:117382000-117387600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:117382000-117388000	Strong transcription	Osteobl	bone
39	chr12:117382000-117388400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:117382000-117388600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:117382000-117391400	Strong transcription	Fetal Stomach	stomach
42	chr12:117382000-117396400	Weak transcription	GM12878-XiMat	blood
43	chr12:117382200-117386000	Strong transcription	HepG2	liver
44	chr12:117382200-117387800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:117382400-117384000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:117382400-117385200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:117382400-117387800	Strong transcription	Fetal Intestine Small	intestine
48	chr12:117382400-117389400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:117382400-117390400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:117382400-117390600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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