Variant report

Variant	rs368416
Chromosome Location	chr15:74514653-74514654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74504672..74507489-chr15:74514073..74516992,2	MCF-7	breast:
2	chr15:74513953..74515786-chr15:74517220..74519970,2	K562	blood:
3	chr15:74489985..74491760-chr15:74513574..74516077,2	MCF-7	breast:
4	chr15:74514536..74518272-chr15:74526056..74529692,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140481	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11632233	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs11639316	0.80[ASN][1000 genomes]
rs12913651	0.80[JPT][hapmap]
rs16966903	0.82[JPT][hapmap]
rs351178	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351180	0.80[ASN][1000 genomes]
rs351181	0.80[ASN][1000 genomes]
rs392267	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55859302	0.96[ASN][1000 genomes]
rs748608	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs368416	MYO9A	cis	cerebellum	SCAN
rs368416	PARP6	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74506600-74520400	Weak transcription	Left Ventricle	heart
2	chr15:74512200-74515200	Enhancers	Fetal Brain Female	brain
3	chr15:74512200-74515400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:74512200-74516600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:74512200-74518800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:74512200-74522600	Enhancers	Fetal Brain Male	brain
7	chr15:74512400-74515200	Enhancers	Brain Germinal Matrix	brain
8	chr15:74512400-74517800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:74512400-74517800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:74512400-74518800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr15:74512600-74515000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr15:74512600-74515600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr15:74512600-74516800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr15:74512600-74517600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr15:74512600-74517600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:74512600-74517800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:74512800-74514800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
18	chr15:74512800-74518600	Enhancers	Fetal Thymus	thymus
19	chr15:74513000-74515200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr15:74513000-74515400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr15:74513000-74517000	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr15:74513000-74517400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:74513200-74515200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr15:74513600-74515600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:74513600-74516800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:74513800-74515600	Enhancers	Brain Cingulate Gyrus	brain
27	chr15:74514000-74515000	Bivalent Enhancer	Brain Hippocampus Middle	brain
28	chr15:74514000-74517200	Enhancers	Primary T cells from cord blood	blood
29	chr15:74514200-74514800	Enhancers	HSMMtube	muscle
30	chr15:74514200-74515000	Enhancers	HSMM	muscle
31	chr15:74514200-74515400	Weak transcription	Fetal Kidney	kidney
32	chr15:74514400-74514800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr15:74514400-74515800	Weak transcription	Fetal Heart	heart
34	chr15:74514400-74516000	Weak transcription	Thymus	Thymus
35	chr15:74514600-74515000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:74514600-74515000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:74514600-74515200	Weak transcription	Fetal Lung	lung
38	chr15:74514600-74515400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr15:74514600-74515600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:74514600-74518400	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links