Variant report

Variant	rs7539662
Chromosome Location	chr1:227511329-227511330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227510419..227513030-chr1:227581221..227583302,2	K562	blood:
2	chr1:227510624..227512509-chr1:227521394..227523406,2	K562	blood:
3	chr1:227511186..227513689-chr1:227514220..227516640,3	K562	blood:
4	chr1:227509361..227511694-chr1:227523759..227526686,3	K562	blood:
5	chr1:227511205..227513066-chr1:227516243..227518388,2	MCF-7	breast:
6	chr1:227510287..227513038-chr1:227518818..227521633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234277	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10916112	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916113	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916116	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916125	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11576239	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11584325	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11585910	0.96[AMR][1000 genomes]
rs12119153	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12123597	0.81[AMR][1000 genomes]
rs12128174	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12131061	0.89[AMR][1000 genomes]
rs12131459	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12131933	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133230	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133633	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12138092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138364	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138383	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12138664	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12144205	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12746316	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12754677	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12755770	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1513607	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1513613	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17613235	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2063661	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28648445	0.96[AMR][1000 genomes]
rs34113967	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34702208	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34897490	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35160496	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35952573	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4308948	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs61834323	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61834324	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61834326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61834590	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834625	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834626	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6660168	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6675408	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6675572	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6678714	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6697583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512871	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7518813	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523759	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543419	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7548118	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7539662	CNIH4	cis	cerebellum	SCAN
rs7539662	CABC1	cis	parietal	SCAN
rs7539662	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:227508400-227512200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:227509400-227511600	Enhancers	Stomach Mucosa	stomach
5	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:227510000-227511800	Enhancers	Fetal Intestine Small	intestine
7	chr1:227510000-227511800	Enhancers	Pancreas	Pancrea
8	chr1:227510200-227511400	Enhancers	Fetal Intestine Large	intestine
9	chr1:227510200-227511600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:227510200-227511800	Enhancers	Gastric	stomach
11	chr1:227510400-227511400	Weak transcription	Colonic Mucosa	Colon
12	chr1:227510400-227511600	Enhancers	K562	blood
13	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:227510800-227511800	Enhancers	NHEK	skin
15	chr1:227510800-227512200	Flanking Active TSS	Hela-S3	cervix
16	chr1:227511000-227511800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:227511200-227511400	Flanking Active TSS	Liver	Liver
18	chr1:227511200-227511400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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