Variant report

Variant	rs4902479
Chromosome Location	chr14:67998204-67998205
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:67997332..67999745-chr14:68050873..68052714,2	MCF-7	breast:
2	chr14:67991794..67994856-chr14:67997202..67999536,4	K562	blood:
3	chr14:67998150..68002925-chr14:68034555..68041423,8	MCF-7	breast:
4	chr14:67980933..67983898-chr14:67998089..68001326,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11158681	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11158682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158683	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11158684	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12434659	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782224	0.83[CEU][hapmap]
rs2064929	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4144498	0.84[MEX][hapmap];0.86[YRI][hapmap]
rs4902478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902482	0.84[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902483	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4902484	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4902486	0.88[EUR][1000 genomes]
rs6573780	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7147529	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154636	0.84[EUR][1000 genomes]
rs7155887	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs731681	0.85[GIH][hapmap];0.84[MEX][hapmap]
rs753683	0.87[CEU][hapmap]

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	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4902479	PLEKHH1	cis	cerebellum	SCAN
rs4902479	ADAM20	cis	cerebellum	SCAN
rs4902479	C14orf181	cis	cerebellum	SCAN
rs4902479	FUT8	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67982600-67999000	Weak transcription	Right Atrium	heart
2	chr14:67991600-67999000	Weak transcription	Stomach Mucosa	stomach
3	chr14:67991800-67998800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr14:67993200-67998600	Enhancers	Brain Hippocampus Middle	brain
5	chr14:67993200-67999000	Enhancers	Brain Substantia Nigra	brain
6	chr14:67994000-67998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:67994000-67998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr14:67994000-67998800	Weak transcription	Fetal Intestine Small	intestine
9	chr14:67994000-67999000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:67994000-67999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:67994000-67999000	Weak transcription	Fetal Intestine Large	intestine
12	chr14:67994800-67999200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:67995200-67999000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr14:67997200-67998600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr14:67997400-67999200	Enhancers	Placenta	Placenta
16	chr14:67997800-67998600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr14:67998000-67998600	Weak transcription	Brain Angular Gyrus	brain
18	chr14:67998200-67998600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:67998200-67998600	Weak transcription	Pancreas	Pancrea
20	chr14:67998200-67998800	Enhancers	Brain Anterior Caudate	brain
21	chr14:67998200-67999400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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