Variant report

Variant	rs12914098
Chromosome Location	chr15:77823013-77823014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77816521..77820074-chr15:77822990..77824875,3	K562	blood:
2	chr15:77822048..77824496-chr15:77832446..77834927,2	K562	blood:
3	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
4	chr15:77822210..77823977-chr15:77824433..77827126,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259362	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11630540	0.94[ASN][1000 genomes]
rs11630557	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630916	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630926	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631274	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632602	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634174	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635567	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635606	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639293	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898370	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12898656	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12899390	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901100	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901338	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901471	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901732	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901765	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901998	0.94[ASN][1000 genomes]
rs12902379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902698	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902852	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902896	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902912	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902925	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904212	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904254	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904348	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904584	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904709	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904823	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909292	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909645	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909808	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910512	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910513	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910594	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910951	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12910975	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911649	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12911854	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911963	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912386	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914932	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915548	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916515	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916642	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916682	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12916822	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916833	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916973	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12917175	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917314	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17394732	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34020536	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34829483	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35284122	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35577135	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59418918	0.94[ASN][1000 genomes]
rs62007348	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62007350	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62009067	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62009071	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62009087	0.94[ASN][1000 genomes]
rs7176307	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176875	0.96[ASN][1000 genomes]
rs7180732	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181283	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025968	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027056	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8032405	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033067	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033654	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040318	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8040702	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8041398	0.91[ASN][1000 genomes]
rs8041520	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8042307	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12914098	RP11-307C19.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77816400-77823400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:77817200-77824000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:77817600-77824800	Enhancers	Placenta	Placenta
4	chr15:77817800-77823400	Enhancers	Fetal Muscle Trunk	muscle
5	chr15:77817800-77824200	Enhancers	Fetal Muscle Leg	muscle
6	chr15:77818600-77823400	Enhancers	Fetal Intestine Large	intestine
7	chr15:77819600-77828600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:77819800-77831000	Weak transcription	Gastric	stomach
9	chr15:77820200-77823600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:77820600-77823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:77820800-77826200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:77821000-77825600	Weak transcription	Fetal Brain Female	brain
13	chr15:77821000-77825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:77821000-77825800	Enhancers	Spleen	Spleen
15	chr15:77821000-77826800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
17	chr15:77821400-77823200	Genic enhancers	Fetal Intestine Small	intestine
18	chr15:77821400-77825200	Weak transcription	Brain Germinal Matrix	brain
19	chr15:77821400-77826000	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:77821600-77823600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr15:77821600-77825200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:77821600-77825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:77821600-77825400	Weak transcription	Fetal Brain Male	brain
24	chr15:77821600-77826000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:77821600-77830200	Weak transcription	Left Ventricle	heart
26	chr15:77821800-77825000	Weak transcription	Fetal Kidney	kidney
27	chr15:77821800-77827600	Weak transcription	Pancreas	Pancrea
28	chr15:77822000-77824200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:77822000-77825200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:77822000-77825400	Weak transcription	Right Ventricle	heart
31	chr15:77822000-77825600	Weak transcription	Fetal Heart	heart
32	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
33	chr15:77822200-77825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:77822400-77823200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:77822400-77824600	Enhancers	HepG2	liver
36	chr15:77822400-77825200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:77822400-77825400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:77822400-77825400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:77822400-77825400	Weak transcription	Fetal Lung	lung
40	chr15:77822400-77825600	Weak transcription	Ovary	ovary
41	chr15:77822600-77823600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:77822600-77823600	Weak transcription	Fetal Stomach	stomach
43	chr15:77822600-77825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:77822800-77823200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:77823000-77823200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:77823000-77823200	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links