Variant report

Variant	rs3768547
Chromosome Location	chr1:212871081-212871082
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212779956..212785175-chr1:212870276..212874748,7	K562	blood:
2	chr1:212866207..212868017-chr1:212869648..212871238,2	K562	blood:
3	chr1:212790623..212792984-chr1:212868720..212871202,2	K562	blood:
4	chr1:212865556..212867815-chr1:212870063..212872235,2	MCF-7	breast:
5	chr1:212779956..212783547-chr1:212870276..212874584,4	K562	blood:
6	chr1:212860743..212863058-chr1:212869735..212872128,3	K562	blood:

Variant related genes	Relation type
ENSG00000123685	Chromatin interaction
ENSG00000207491	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12128789	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs12133919	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202683	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2221593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73079851	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3768547	NSL1	cis	parietal	SCAN
rs3768547	BATF3	cis	lymphoblastoid	seeQTL
rs3768547	CD55	cis	parietal	SCAN
rs3768547	BATF3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212857200-212871600	Weak transcription	Dnd41	blood
2	chr1:212858600-212872200	Weak transcription	Gastric	stomach
3	chr1:212858800-212872200	Weak transcription	Aorta	Aorta
4	chr1:212862600-212871600	Weak transcription	NHLF	lung
5	chr1:212863400-212872200	Weak transcription	Spleen	Spleen
6	chr1:212866800-212871800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:212867000-212872200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:212867200-212871800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:212869400-212872000	Weak transcription	Right Atrium	heart
10	chr1:212870000-212872600	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:212870200-212872200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:212870400-212871200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr1:212870400-212872000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:212870400-212872000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:212870800-212871800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:212870800-212872000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:212871000-212871200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:212871000-212871200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:212871000-212871600	Bivalent Enhancer	Primary T cells from cord blood	blood
20	chr1:212871000-212872000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:212871000-212872000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:212871000-212872000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:212871000-212872000	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links