Variant report

Variant	rs12898656
Chromosome Location	chr15:77807995-77807996
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	chr15:77806711..77809652-chr15:77816101..77819941,3	MCF-7	breast:
2	chr15:77793912..77796870-chr15:77807695..77810216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259362	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10519167	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs11629652	0.92[ASN][1000 genomes]
rs11629835	0.92[ASN][1000 genomes]
rs11630557	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630916	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630926	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631274	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632602	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632729	0.84[JPT][hapmap]
rs11634174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635567	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635606	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636412	0.89[ASN][1000 genomes]
rs11636529	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11639293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898281	0.91[ASN][1000 genomes]
rs12898370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899390	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901100	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901338	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901471	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901732	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901765	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902072	0.88[CEU][hapmap]
rs12902379	0.80[AMR][1000 genomes]
rs12902698	1.00[CEU][hapmap];0.89[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902898	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12902912	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902925	0.92[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904212	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904254	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]
rs12904348	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904584	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904823	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12909292	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap]
rs12909645	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909808	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910512	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910594	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910951	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910975	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911649	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911854	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912386	0.92[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914098	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12914932	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs12915548	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916515	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916642	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916682	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916822	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916833	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916973	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917044	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12917175	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12917314	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16968835	0.84[JPT][hapmap]
rs17394732	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs34020536	0.92[AMR][1000 genomes];0.91[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	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007348	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007350	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009067	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62009069	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62009071	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119	0.84[JPT][hapmap]
rs7176307	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7180732	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7181283	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025968	0.88[CEU][hapmap]
rs8027056	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032071	0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8032405	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033067	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033654	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8040318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042307	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12898656	HMG20A	cis	parietal	SCAN
rs12898656	SGK269	cis	parietal	SCAN
rs12898656	HMG20A	cis	cerebellum	SCAN
rs12898656	RP11-307C19.1	cis	Heart Left Ventricle	GTEx
rs12898656	STRA6	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77800400-77819600	Weak transcription	Fetal Brain Female	brain
2	chr15:77801000-77818800	Weak transcription	Fetal Intestine Small	intestine
3	chr15:77801400-77820000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77801600-77821400	Weak transcription	Pancreas	Pancrea
5	chr15:77802600-77820000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:77803200-77808600	Weak transcription	Spleen	Spleen
7	chr15:77803200-77809200	Weak transcription	Right Atrium	heart
8	chr15:77803200-77819200	Weak transcription	Lung	lung
9	chr15:77803400-77808200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:77803400-77809200	Weak transcription	Placenta	Placenta
11	chr15:77803800-77811400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:77804000-77811200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:77804200-77808000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:77804200-77819400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:77804200-77819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:77806600-77808000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr15:77806800-77808200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:77807000-77808200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:77807000-77808200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:77807000-77808200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:77807000-77808200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:77807000-77808200	Enhancers	Left Ventricle	heart
23	chr15:77807000-77808400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr15:77807000-77808400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:77807000-77808400	Enhancers	Brain Substantia Nigra	brain
26	chr15:77807000-77808600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:77807000-77808600	Enhancers	Brain Anterior Caudate	brain
28	chr15:77807000-77808600	Enhancers	Brain Cingulate Gyrus	brain
29	chr15:77807000-77810800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:77807200-77808200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr15:77807200-77808600	Enhancers	Brain Hippocampus Middle	brain
32	chr15:77807400-77811000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:77807400-77819400	Weak transcription	Right Ventricle	heart
34	chr15:77807600-77808000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:77807600-77810400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:77807600-77819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links