Variant report

Variant	rs10192894
Chromosome Location	chr2:62838936-62838937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM17-2	chr2:62838524-62839358	XLOC_002117
2	lnc-TMEM17-2	chr2:62838524-62839358	XLOC_002117
3	lnc-TMEM17-2	chr2:62838915-62839358	XLOC_002117
4	lnc-EHBP1-2	chr2:62838914-62839358	NONHSAT071024
5	lnc-TMEM17-2	chr2:62838524-62839358	XLOC_002117

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10186082	0.89[ASN][1000 genomes]
rs10204410	0.96[ASN][1000 genomes]
rs11125929	0.95[ASN][1000 genomes]
rs11125930	0.84[ASN][1000 genomes]
rs13404126	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13417156	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1386401	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1406002	0.90[ASN][1000 genomes]
rs1601673	0.95[ASN][1000 genomes]
rs28798215	0.91[ASN][1000 genomes]
rs62180020	0.93[ASN][1000 genomes]
rs6545960	0.85[ASN][1000 genomes]
rs6545961	0.90[ASN][1000 genomes]
rs6545962	0.96[ASN][1000 genomes]
rs6545963	0.92[ASN][1000 genomes]
rs6714927	0.95[ASN][1000 genomes]
rs6752597	0.91[ASN][1000 genomes]
rs7558681	0.98[ASN][1000 genomes]
rs7564277	0.81[ASN][1000 genomes]
rs7578229	0.92[ASN][1000 genomes]
rs7583570	0.95[ASN][1000 genomes]
rs7607678	0.82[ASN][1000 genomes]
rs9989741	0.95[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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10192894	MDH1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62825400-62839000	Weak transcription	Osteobl	bone
2	chr2:62831800-62839000	Weak transcription	NHDF-Ad	bronchial
3	chr2:62832200-62868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:62838600-62840200	Enhancers	Fetal Brain Male	brain
5	chr2:62838800-62839200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:62838800-62839400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:62838800-62839600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:62838800-62839600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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