Variant report

Variant	rs351386
Chromosome Location	chr1:212421771-212421772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212420552..212422423-chr1:212423039..212425557,2	K562	blood:
2	chr1:212414204..212417772-chr1:212418799..212421886,6	K562	blood:
3	chr1:212407788..212409741-chr1:212419930..212421774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap]
rs1009622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs11119884	0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11119885	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11119887	0.86[ASN][1000 genomes]
rs11119904	0.83[EUR][1000 genomes]
rs12033246	1.00[CEU][hapmap]
rs12035647	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12036130	0.86[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap]
rs1389369	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1389371	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472226	0.83[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs17042034	0.83[EUR][1000 genomes]
rs1774249	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs1967117	0.80[ASN][1000 genomes]
rs1992643	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2001234	0.82[ASN][1000 genomes]
rs2012917	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2087946	0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2252044	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs2516331	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589474	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884512	0.80[ASN][1000 genomes]
rs3099112	1.00[CEU][hapmap]
rs351373	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351377	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351378	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351379	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351380	0.82[EUR][1000 genomes]
rs351393	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs351398	0.81[EUR][1000 genomes]
rs351401	0.83[EUR][1000 genomes]
rs351407	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351408	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]
rs351417	0.86[EUR][1000 genomes]
rs351419	0.89[EUR][1000 genomes]
rs3767861	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs3767862	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs4362041	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs4951582	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951583	0.88[GIH][hapmap]
rs4951589	1.00[CEU][hapmap]
rs6540731	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs6540732	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs6540733	0.83[CHB][hapmap]
rs6657900	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs6668866	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6679796	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7415843	1.00[CEU][hapmap]
rs7519168	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7519959	1.00[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs7544225	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867584	0.81[ASN][1000 genomes]
rs903120	0.80[ASN][1000 genomes]
rs903121	0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs951623	0.80[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
rs351386	LGTN	cis	cerebellum	SCAN
rs351386	TMEM206	cis	parietal	SCAN
rs351386	SLC30A1	cis	cerebellum	SCAN
rs351386	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs351386	SYT14	cis	cerebellum	SCAN
rs351386	TMEM206	cis	cerebellum	SCAN
rs351386	TMEM206	cis	Esophagus Mucosa	GTEx
rs351386	CD34	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212416600-212430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212418000-212423800	Weak transcription	Stomach Mucosa	stomach
3	chr1:212418200-212428400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:212419600-212422400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:212419800-212425200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:212420600-212421800	Enhancers	Fetal Lung	lung
7	chr1:212420600-212422000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:212420800-212421800	Enhancers	Liver	Liver
9	chr1:212420800-212422000	Enhancers	Fetal Intestine Large	intestine
10	chr1:212420800-212422000	Enhancers	Fetal Intestine Small	intestine
11	chr1:212421000-212422000	Enhancers	Adipose Nuclei	Adipose
12	chr1:212421000-212422400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:212421000-212423000	Enhancers	HepG2	liver
14	chr1:212421200-212422400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:212421600-212422000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:212421600-212428400	Weak transcription	Right Ventricle	heart

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