Variant report

Variant	rs12599090
Chromosome Location	chr16:12187341-12187342
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12183674..12186424-chr16:12186757..12189168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175604	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11075049	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11075054	0.81[ASN][1000 genomes]
rs11639701	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11642033	0.85[ASN][1000 genomes]
rs11642386	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11646458	0.88[ASN][1000 genomes]
rs11646539	0.81[ASN][1000 genomes]
rs11646584	0.85[ASN][1000 genomes]
rs11647572	0.82[ASN][1000 genomes]
rs11648228	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648468	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648816	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596549	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596703	0.82[ASN][1000 genomes]
rs12599793	0.81[ASN][1000 genomes]
rs12708746	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12926900	0.97[ASN][1000 genomes]
rs12929519	0.85[ASN][1000 genomes]
rs13336687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958964	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457193	0.86[ASN][1000 genomes]
rs28439695	0.87[ASN][1000 genomes]
rs28667047	0.86[ASN][1000 genomes]
rs2869808	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs350264	0.86[ASN][1000 genomes]
rs350265	0.82[ASN][1000 genomes]
rs350266	0.82[ASN][1000 genomes]
rs35053871	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35318501	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35542345	0.85[ASN][1000 genomes]
rs3851011	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851012	0.95[ASN][1000 genomes]
rs4780411	0.98[ASN][1000 genomes]
rs4781180	0.99[ASN][1000 genomes]
rs71385189	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195019	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7200307	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8048589	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050180	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8055516	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8059989	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062015	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8063329	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925009	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9935284	0.81[ASN][1000 genomes]
rs9936270	0.80[ASN][1000 genomes]
rs9939383	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:12178600-12199600	Weak transcription	Aorta	Aorta
3	chr16:12182200-12188600	Weak transcription	Fetal Brain Male	brain
4	chr16:12183800-12189200	Weak transcription	Pancreas	Pancrea
5	chr16:12184000-12189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:12184000-12189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr16:12184000-12189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr16:12184000-12189200	Weak transcription	Liver	Liver
9	chr16:12184000-12189200	Weak transcription	Colon Smooth Muscle	Colon
10	chr16:12184000-12189200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr16:12184000-12189400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr16:12184000-12191600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:12184200-12189000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:12184200-12189000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:12184200-12189200	Weak transcription	Fetal Intestine Large	intestine
18	chr16:12184200-12190400	Enhancers	Thymus	Thymus
19	chr16:12184200-12192200	Weak transcription	Gastric	stomach
20	chr16:12184200-12193000	Enhancers	Fetal Thymus	thymus
21	chr16:12184400-12188200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr16:12184400-12189200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:12184600-12188800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr16:12184600-12188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr16:12184600-12189200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr16:12185000-12187400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:12185000-12188200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr16:12185400-12187400	Enhancers	Spleen	Spleen
30	chr16:12185400-12187400	Enhancers	HUVEC	blood vessel
31	chr16:12185400-12189000	Strong transcription	Primary B cells from cord blood	blood
32	chr16:12185400-12189200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:12185600-12187400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr16:12185800-12187400	Enhancers	Fetal Muscle Leg	muscle
35	chr16:12185800-12187600	Enhancers	Placenta	Placenta
36	chr16:12185800-12187800	Enhancers	HSMMtube	muscle
37	chr16:12186000-12187400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr16:12186000-12188800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr16:12186000-12189800	Weak transcription	Esophagus	oesophagus
40	chr16:12186200-12189200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:12186400-12189400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:12186600-12188800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr16:12186600-12188800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:12186600-12188800	Weak transcription	Fetal Stomach	stomach
45	chr16:12186600-12188800	Weak transcription	K562	blood
46	chr16:12186600-12189200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:12186600-12189200	Weak transcription	A549	lung
48	chr16:12186600-12189400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr16:12186600-12189400	Weak transcription	Fetal Kidney	kidney
50	chr16:12186600-12189800	Weak transcription	Small Intestine	intestine

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