Variant report

Variant	rs3008653
Chromosome Location	chr1:222764791-222764792
allele	C/G
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	chr1:222764659-222764833	K562	blood:	n/a	chr1:222764747-222764760
2	IRF1	chr1:222764643-222764833	K562	blood:	n/a	n/a
3	ZNF143	chr1:222764723-222764957	K562	blood:	n/a	chr1:222764832-222764851

No.	Distal block	Cell Line	Cell type
1	chr1:222763603..222766024-chr1:222777146..222778835,2	K562	blood:
2	chr1:222761959..222766700-chr1:222790061..222794365,7	MCF-7	breast:
3	chr1:222761567..222764879-chr1:222790132..222793494,4	MCF-7	breast:
4	chr1:222759001..222761767-chr1:222763501..222765317,2	MCF-7	breast:
5	chr1:222760723..222765796-chr1:222790714..222795393,9	K562	blood:

Variant related genes	Relation type
TAF1A	TF binding region
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1024065	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10495194	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17463740	0.93[EUR][1000 genomes]
rs17464857	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17511318	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1909194	0.90[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982983	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2006790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936030	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936044	0.89[EUR][1000 genomes]
rs2936045	0.89[EUR][1000 genomes]
rs2936046	0.89[EUR][1000 genomes]
rs3002130	0.90[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008594	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs3008645	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3008647	0.83[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008654	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008655	0.87[EUR][1000 genomes]
rs35750438	0.93[EUR][1000 genomes]
rs3748625	0.97[ASN][1000 genomes]
rs3828060	0.97[ASN][1000 genomes]
rs4328077	0.91[EUR][1000 genomes]
rs73122816	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122823	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73122834	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122837	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122849	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122850	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122857	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74145503	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74148133	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74148140	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74148142	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9441828	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9441911	0.91[EUR][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	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222764000-222765200	Weak transcription	NHDF-Ad	bronchial
2	chr1:222764000-222766400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:222764000-222766400	Weak transcription	Ovary	ovary
4	chr1:222764000-222767800	Weak transcription	Gastric	stomach
5	chr1:222764000-222768200	Weak transcription	Fetal Kidney	kidney
6	chr1:222764000-222773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:222764200-222765200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:222764200-222765400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:222764200-222765400	Weak transcription	HSMM	muscle
10	chr1:222764200-222765400	Weak transcription	NH-A	brain
11	chr1:222764200-222765400	Weak transcription	Osteobl	bone
12	chr1:222764200-222765600	Enhancers	K562	blood
13	chr1:222764200-222769800	Weak transcription	Fetal Heart	heart
14	chr1:222764400-222765600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:222764400-222768800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:222764400-222769200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:222764600-222768400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links