Variant report

Variant	rs12904254
Chromosome Location	chr15:77802585-77802586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77797715..77799505-chr15:77800913..77803118,3	MCF-7	breast:
2	chr15:77801166..77802677-chr15:77810590..77812959,2	MCF-7	breast:
3	chr15:77800783..77803044-chr15:77808974..77810922,2	K562	blood:
4	chr15:77800020..77805731-chr15:77808908..77813033,5	MCF-7	breast:
5	chr15:77787813..77789650-chr15:77801931..77804877,2	K562	blood:
6	chr15:77802309..77804829-chr15:77815789..77819880,3	MCF-7	breast:
7	chr15:77798766..77801292-chr15:77802279..77806455,3	K562	blood:

Variant related genes	Relation type
ENSG00000259362	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10519167	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11629652	0.92[ASN][1000 genomes]
rs11629835	0.92[ASN][1000 genomes]
rs11630557	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630916	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630926	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631274	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632602	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635567	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635606	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636412	0.89[ASN][1000 genomes]
rs11636529	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11639293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898281	0.91[ASN][1000 genomes]
rs12898370	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898656	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899390	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901100	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901338	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901471	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901732	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901765	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902698	0.85[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902852	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902912	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902925	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904212	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904348	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904584	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904709	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904823	0.88[JPT][hapmap]
rs12909292	0.86[JPT][hapmap]
rs12909645	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909808	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910512	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910513	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910594	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910975	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911649	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911854	0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911963	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912386	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914098	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12914932	0.88[JPT][hapmap]
rs12915548	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916515	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916642	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916822	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916833	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917175	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12917314	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17394732	0.86[JPT][hapmap]
rs34020536	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34194537	0.94[ASN][1000 genomes]
rs35235292	0.81[ASN][1000 genomes]
rs35268067	0.84[ASN][1000 genomes]
rs35284122	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007348	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007350	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009067	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62009069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62009071	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176307	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7180732	0.85[EUR][1000 genomes]
rs7181283	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025968	0.88[JPT][hapmap]
rs8027056	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032071	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs8032405	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033067	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033654	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8040318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042307	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12904254	RP11-307C19.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77786400-77803800	Weak transcription	Primary T cells from cord blood	blood
2	chr15:77795400-77803000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:77796600-77803800	Enhancers	Left Ventricle	heart
4	chr15:77796600-77804200	Enhancers	Fetal Heart	heart
5	chr15:77797000-77803200	Enhancers	Lung	lung
6	chr15:77797000-77803400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:77797000-77803800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:77797200-77803200	Enhancers	Right Atrium	heart
9	chr15:77798000-77803200	Enhancers	Spleen	Spleen
10	chr15:77798200-77802600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:77798400-77803400	Enhancers	Fetal Muscle Trunk	muscle
12	chr15:77798400-77803800	Enhancers	Fetal Muscle Leg	muscle
13	chr15:77799000-77803800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:77799000-77803800	Enhancers	Psoas Muscle	Psoas
15	chr15:77800200-77803400	Enhancers	Right Ventricle	heart
16	chr15:77800200-77804200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr15:77800200-77805800	Weak transcription	Fetal Brain Male	brain
18	chr15:77800400-77803800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:77800400-77804200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr15:77800400-77819600	Weak transcription	Fetal Brain Female	brain
21	chr15:77800600-77804000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:77800600-77807000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:77800800-77803000	Enhancers	Brain Hippocampus Middle	brain
24	chr15:77800800-77803400	Enhancers	Adipose Nuclei	Adipose
25	chr15:77800800-77804200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr15:77800800-77804200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:77801000-77802800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr15:77801000-77818800	Weak transcription	Fetal Intestine Small	intestine
29	chr15:77801400-77802600	Enhancers	HepG2	liver
30	chr15:77801400-77803000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:77801400-77803600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:77801400-77820000	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:77801600-77802600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:77801600-77802600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:77801600-77802600	Weak transcription	Ovary	ovary
36	chr15:77801600-77802800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:77801600-77802800	Enhancers	Brain Substantia Nigra	brain
38	chr15:77801600-77803600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:77801600-77804000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr15:77801600-77821400	Weak transcription	Pancreas	Pancrea
41	chr15:77801800-77802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:77801800-77802800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:77801800-77803200	Weak transcription	Fetal Lung	lung
44	chr15:77801800-77803200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:77801800-77805400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:77801800-77806000	Weak transcription	HUVEC	blood vessel
47	chr15:77801800-77807000	Weak transcription	Brain Anterior Caudate	brain
48	chr15:77801800-77807200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr15:77801800-77807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:77802400-77802800	Active TSS	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links