Variant report

Variant	rs12899303
Chromosome Location	chr15:76051656-76051657
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	chr15:76050716..76052261-chr15:76053754..76055876,2	K562	blood:
2	chr15:76038205..76040271-chr15:76051114..76054097,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC019294.2-1	chr15:76050881-76052477	ENSG00000260288.1

Variant related genes	Relation type
ENSG00000261043	Chromatin interaction
ENSG00000260815	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10163112	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10519109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852472	0.82[ASN][1000 genomes]
rs11852712	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854305	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11858818	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898509	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899163	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12900007	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900167	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904654	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905730	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13329104	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1823175	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1850261	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1964473	0.89[ASN][1000 genomes]
rs1964474	0.88[ASN][1000 genomes]
rs1996302	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996303	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002668	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2004630	0.88[ASN][1000 genomes]
rs2004920	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009508	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010392	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2017312	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2405718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405719	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2405882	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28404806	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28541422	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615348	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28651447	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657001	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688252	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695212	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695716	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28744558	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28833005	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28837134	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243492	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34402412	0.85[EUR][1000 genomes]
rs34469290	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34571038	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34605750	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611707	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34909574	0.81[ASN][1000 genomes]
rs34941412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35019194	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35135316	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35136767	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35147271	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35237189	0.82[ASN][1000 genomes]
rs35411779	0.85[ASN][1000 genomes]
rs35575236	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35745834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35842909	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880865	0.82[ASN][1000 genomes]
rs36057011	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751536	0.82[ASN][1000 genomes]
rs3845233	0.88[ASN][1000 genomes]
rs3845234	0.88[ASN][1000 genomes]
rs3850092	0.89[ASN][1000 genomes]
rs3861184	0.91[ASN][1000 genomes]
rs4503758	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55744943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57905971	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60214227	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66838310	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs67908345	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71403504	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71403505	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71462532	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163633	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165531	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181595	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026532	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027311	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028002	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037672	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8041390	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8041670	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
3	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv974599	chr15:76033068-76101142	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76050000-76051800	Active TSS	Fetal Kidney	kidney
2	chr15:76050200-76051800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:76050200-76051800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:76050200-76051800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:76050400-76051800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:76050400-76051800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:76050400-76051800	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:76051200-76051800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:76051200-76051800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:76051200-76051800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:76051200-76051800	Flanking Active TSS	Fetal Thymus	thymus
12	chr15:76051200-76052000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:76051200-76052200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:76051200-76052200	Enhancers	Stomach Mucosa	stomach
15	chr15:76051200-76052600	Weak transcription	Spleen	Spleen
16	chr15:76051400-76051800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:76051400-76051800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:76051400-76051800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr15:76051400-76051800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr15:76051400-76051800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr15:76051400-76051800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:76051400-76051800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr15:76051400-76051800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr15:76051400-76051800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr15:76051400-76051800	Enhancers	Colon Smooth Muscle	Colon
26	chr15:76051400-76051800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:76051400-76051800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr15:76051400-76051800	Flanking Active TSS	A549	lung
29	chr15:76051400-76051800	Enhancers	HepG2	liver
30	chr15:76051400-76051800	Enhancers	HSMMtube	muscle
31	chr15:76051400-76052000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:76051400-76052000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr15:76051400-76052200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:76051400-76052200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:76051400-76052200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr15:76051400-76052200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:76051400-76052200	Flanking Active TSS	Dnd41	blood
38	chr15:76051400-76052400	Enhancers	Primary B cells from peripheral blood	blood
39	chr15:76051400-76052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:76051400-76052600	Weak transcription	Left Ventricle	heart
41	chr15:76051400-76053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:76051400-76054000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:76051400-76055600	Weak transcription	Pancreas	Pancrea
44	chr15:76051400-76057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:76051400-76059000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:76051400-76063200	Weak transcription	Right Atrium	heart
47	chr15:76051600-76051800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:76051600-76051800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr15:76051600-76051800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:76051600-76051800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links