Variant report

Variant	rs6702036
Chromosome Location	chr1:94151589-94151590
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:94151528-94151820	GM12891	blood:	n/a	n/a
2	MEF2A	chr1:94151346-94151871	GM12878	blood:	n/a	n/a
3	SPI1	chr1:94151510-94151766	GM12878	blood:	n/a	n/a
4	SPI1	chr1:94151485-94151881	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94151003..94153408-chr1:94159847..94162420,2	MCF-7	breast:
2	chr1:94088742..94090427-chr1:94150659..94152281,2	K562	blood:
3	chr1:94150767..94155477-chr1:94157317..94159691,6	MCF-7	breast:

Variant related genes	Relation type
BCAR3	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1011903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12057736	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12079723	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084853	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12568405	1.00[JPT][hapmap]
rs1292929	0.91[ASN][1000 genomes]
rs1567791	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1772781	1.00[JPT][hapmap]
rs236266	1.00[JPT][hapmap]
rs236284	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs236285	0.86[ASN][1000 genomes]
rs236287	0.87[CEU][hapmap];0.86[ASN][1000 genomes]
rs236288	0.91[ASN][1000 genomes]
rs236291	0.91[ASN][1000 genomes]
rs236292	0.88[ASN][1000 genomes]
rs236295	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs236296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236301	0.91[ASN][1000 genomes]
rs236308	0.90[JPT][hapmap]
rs236312	1.00[JPT][hapmap]
rs236313	1.00[JPT][hapmap]
rs236343	0.89[JPT][hapmap]
rs236344	0.80[MEX][hapmap]
rs3767979	0.89[JPT][hapmap]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[JPT][hapmap]
rs423493	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs61781002	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6660740	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6701871	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704479	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7513130	0.85[CEU][hapmap]
rs7519952	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798213	1.00[JPT][hapmap]
rs955470	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659100	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6702036	SNORD21	cis	cerebellum	SCAN
rs6702036	F3	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94147800-94153200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:94148000-94151600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:94148200-94151800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94148200-94151800	Weak transcription	A549	lung
5	chr1:94148200-94151800	Weak transcription	HepG2	liver
6	chr1:94148200-94152000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:94148200-94152200	Weak transcription	HUVEC	blood vessel
8	chr1:94148200-94154600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:94148200-94154600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:94148200-94155200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:94148200-94156800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:94148200-94156800	Weak transcription	NHLF	lung
13	chr1:94148200-94167200	Weak transcription	Right Atrium	heart
14	chr1:94148400-94151800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:94148400-94152200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:94148400-94152200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:94148400-94156200	Weak transcription	HSMM	muscle
18	chr1:94148400-94156600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:94148400-94156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:94148600-94152200	Weak transcription	NHEK	skin
21	chr1:94148800-94156400	Weak transcription	HMEC	breast
22	chr1:94150400-94156000	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:94150800-94152600	Enhancers	Primary B cells from cord blood	blood
24	chr1:94151200-94153600	Enhancers	Hela-S3	cervix
25	chr1:94151400-94151600	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links