Variant report

Variant	rs16869425
Chromosome Location	chr5:90385098-90385099
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90384749..90386468-chr5:90389103..90391299,2	K562	blood:
2	chr5:90383911..90386250-chr5:90677825..90680262,2	K562	blood:
3	chr5:90382535..90385336-chr5:90386183..90388802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12109264	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16869403	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16869404	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16869414	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1852731	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876635	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap]
rs1986718	1.00[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950849	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950850	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2950851	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950852	0.91[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950853	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950854	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950855	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973444	0.90[CEU][hapmap];0.94[YRI][hapmap]
rs2973445	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973447	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973448	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973449	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973450	1.00[CEU][hapmap];0.89[CHD][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973453	1.00[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2973454	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2973455	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2973456	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112484	1.00[CEU][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3952745	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56137437	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56377639	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58524182	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59654682	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59661306	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61392689	1.00[ASN][1000 genomes]
rs66482530	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66608099	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6874106	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73187190	1.00[ASN][1000 genomes]
rs73189008	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16869425	TMEM14C	trans	lymphoblastoid	RTeQTL
rs16869425	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90358400-90391000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:90360200-90386400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:90366600-90386600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:90369400-90386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:90369600-90386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:90370600-90397600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:90380000-90391800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:90384600-90385400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:90384800-90385200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:90384800-90386000	Enhancers	Brain Germinal Matrix	brain
11	chr5:90384800-90387600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr5:90385000-90389000	Weak transcription	Stomach Mucosa	stomach

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