Variant report

Variant	rs606312
Chromosome Location	chr1:120222582-120222583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120222255..120224954-chr1:120226603..120228943,3	K562	blood:
2	chr1:120188672..120190816-chr1:120220429..120222644,2	K562	blood:
3	chr1:120218290..120220840-chr1:120221608..120223374,2	MCF-7	breast:
4	chr1:120216865..120219033-chr1:120220435..120223044,2	K562	blood:
5	chr1:120212453..120214057-chr1:120222058..120224948,2	K562	blood:

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1163251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2764886	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs477992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs478093	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs478450	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs483180	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs483360	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs487081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493427	0.86[CEU][hapmap]
rs496195	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496198	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514491	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517533	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532303	0.89[ASN][1000 genomes]
rs539708	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541503	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs561931	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs592762	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs594400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs595283	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597308	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598685	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611365	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs612430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629735	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639761	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640195	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658442	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs660073	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs662243	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662602	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs666930	0.85[CHD][hapmap]
rs677277	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs839600	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839607	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs839608	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs866321	0.90[AMR][1000 genomes];0.99[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs606312	NBPF7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120218800-120225000	Weak transcription	NHEK	skin
2	chr1:120219000-120226200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:120220800-120224600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:120221400-120222600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr1:120221400-120222800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:120221400-120223200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:120221600-120222600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:120221600-120222800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:120221800-120222800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:120222000-120222600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:120222000-120222800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:120222200-120222600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:120222200-120222600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:120222200-120222600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:120222200-120222600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:120222200-120222800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr1:120222400-120222800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:120222400-120223200	Enhancers	Fetal Intestine Small	intestine

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