Variant report

Variant	rs351408
Chromosome Location	chr1:212441128-212441129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212439869..212442717-chr1:212444447..212446810,3	K562	blood:
2	chr1:212434393..212437066-chr1:212439092..212441986,2	K562	blood:
3	chr1:212433580..212437066-chr1:212438671..212444004,6	K562	blood:
4	chr1:212439329..212443402-chr1:212456167..212459238,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap]
rs1009622	0.91[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs11119884	0.82[CHB][hapmap]
rs11119887	0.80[ASN][1000 genomes]
rs11119904	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12033246	1.00[CEU][hapmap]
rs12035647	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12036130	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12402397	0.83[JPT][hapmap]
rs1389371	0.96[CEU][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1472226	0.82[CHD][hapmap]
rs17042034	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1774249	0.96[CEU][hapmap]
rs1992643	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2252044	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs2516331	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589474	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099112	1.00[CEU][hapmap]
rs351373	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351377	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351378	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351379	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351380	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351386	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351393	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351398	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs351401	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351407	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351417	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs351419	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3767861	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs3767862	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs4951582	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951583	0.85[GIH][hapmap]
rs4951589	1.00[CEU][hapmap]
rs6540731	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs6540732	0.83[JPT][hapmap]
rs6540733	0.83[JPT][hapmap]
rs6668866	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs6679796	0.82[CHB][hapmap]
rs7415843	1.00[CEU][hapmap]
rs7519168	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs7519959	1.00[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs7544225	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs351408	TMEM206	cis	Esophagus Mucosa	GTEx
rs351408	TMEM206	cis	cerebellum	SCAN
rs351408	TMEM206	cis	parietal	SCAN
rs351408	SLC30A1	cis	cerebellum	SCAN
rs351408	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs351408	SYT14	cis	cerebellum	SCAN
rs351408	CD34	cis	cerebellum	SCAN
rs351408	LGTN	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212435200-212445600	Weak transcription	Right Atrium	heart
2	chr1:212435400-212444600	Weak transcription	Stomach Mucosa	stomach
3	chr1:212435600-212444400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:212435800-212444800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:212436000-212442600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:212440800-212441400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:212440800-212441600	Enhancers	GM12878-XiMat	blood

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