Variant report

Variant	rs1965878
Chromosome Location	chr14:69939923-69939924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10083335	0.81[AMR][1000 genomes]
rs10129186	0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs10129720	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10138313	0.82[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs10143593	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs10143710	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10151691	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11622711	0.87[AMR][1000 genomes]
rs11623094	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11624577	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs12147478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12147967	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12436172	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12878175	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs12893282	0.83[AMR][1000 genomes]
rs12895620	0.82[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs1466255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1958121	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs2085193	0.86[AMR][1000 genomes]
rs2100489	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124191	0.82[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs2124192	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2296722	0.88[ASW][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs28401542	0.81[AMR][1000 genomes]
rs28470369	0.83[AMR][1000 genomes]
rs28661733	0.86[AMR][1000 genomes]
rs28879441	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34405286	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34840252	0.88[AMR][1000 genomes]
rs3759770	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759771	0.82[AMR][1000 genomes]
rs4899295	0.88[ASW][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs4902717	0.82[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs4902719	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56392460	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56953348	0.88[AMR][1000 genomes]
rs67502261	0.86[AMR][1000 genomes]
rs7143858	0.83[AMR][1000 genomes]
rs7145944	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs7147362	0.88[AMR][1000 genomes]
rs7147710	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs7150586	0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7160248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010767	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8012954	0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs8014890	0.88[ASW][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs8015317	0.83[AMR][1000 genomes]
rs8015425	0.81[AMR][1000 genomes]
rs8016781	0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs8020817	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs959242	0.82[ASW][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs9796392	0.85[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	esv3396933	chr14:69906914-70001258	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1048882	chr14:69920881-69976694	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052107	chr14:69922552-69969297	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1039230	chr14:69922552-69972002	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1039192	chr14:69922552-69976694	Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv456335	chr14:69928307-69971598	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv564967	chr14:69928307-69971598	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1965878	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL
rs1965878	EVC	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69923600-69950400	Weak transcription	Gastric	stomach
2	chr14:69925400-69942000	Weak transcription	Spleen	Spleen
3	chr14:69925600-69940000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:69925600-69940000	Weak transcription	Hela-S3	cervix
5	chr14:69926000-69940000	Weak transcription	Brain Anterior Caudate	brain
6	chr14:69926000-69940000	Weak transcription	Fetal Intestine Small	intestine
7	chr14:69928000-69941000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:69928600-69950600	Weak transcription	Aorta	Aorta
9	chr14:69928800-69940200	Weak transcription	Thymus	Thymus
10	chr14:69928800-69940400	Weak transcription	Adipose Nuclei	Adipose
11	chr14:69928800-69941000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:69929000-69940200	Weak transcription	HSMMtube	muscle
13	chr14:69929000-69940400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:69929000-69941400	Weak transcription	Ovary	ovary
15	chr14:69929400-69940200	Weak transcription	Placenta	Placenta
16	chr14:69931800-69940000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:69936200-69940200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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