Variant report

Variant	rs3856020
Chromosome Location	chr1:153019087-153019088
allele	A/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	FOS	chr1:153018939-153019424	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:153018964-153019284	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:153018939-153019362	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:153018934-153019307	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:153018936-153019284	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:153018899-153019299	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:153019001-153019356	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:153019001-153019424	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr1:153018905-153019290	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr1:153018888-153019356	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr1:153019006-153019251	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SPRR2D	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10494288	1.00[EUR][1000 genomes]
rs10888521	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11205130	1.00[EUR][1000 genomes]
rs11205147	1.00[EUR][1000 genomes]
rs11205183	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11806470	1.00[EUR][1000 genomes]
rs12024694	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029192	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12032522	1.00[EUR][1000 genomes]
rs12036697	1.00[EUR][1000 genomes]
rs12037754	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12046394	0.99[ASN][1000 genomes]
rs12047099	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047187	0.99[ASN][1000 genomes]
rs12047225	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047630	1.00[EUR][1000 genomes]
rs12239812	1.00[EUR][1000 genomes]
rs1415973	1.00[EUR][1000 genomes]
rs167452	0.92[ASN][1000 genomes]
rs16834746	1.00[EUR][1000 genomes]
rs16834838	1.00[EUR][1000 genomes]
rs16834871	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1846857	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974141	1.00[EUR][1000 genomes]
rs1995307	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339501	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310096	0.92[ASN][1000 genomes]
rs310097	0.92[ASN][1000 genomes]
rs310098	0.92[ASN][1000 genomes]
rs310099	0.92[ASN][1000 genomes]
rs310101	0.92[ASN][1000 genomes]
rs310104	0.92[ASN][1000 genomes]
rs310112	0.83[ASN][1000 genomes]
rs310113	0.84[ASN][1000 genomes]
rs310116	0.84[ASN][1000 genomes]
rs310117	0.84[ASN][1000 genomes]
rs310125	1.00[ASN][1000 genomes]
rs36090881	1.00[EUR][1000 genomes]
rs367220	0.90[ASN][1000 genomes]
rs373451	0.90[ASN][1000 genomes]
rs374170	0.90[ASN][1000 genomes]
rs377182	0.90[ASN][1000 genomes]
rs399274	0.90[ASN][1000 genomes]
rs4041337	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4041340	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240864	1.00[EUR][1000 genomes]
rs442209	0.91[ASN][1000 genomes]
rs4845328	1.00[EUR][1000 genomes]
rs4845498	1.00[EUR][1000 genomes]
rs576793	0.92[ASN][1000 genomes]
rs58290373	1.00[EUR][1000 genomes]
rs593671	0.92[ASN][1000 genomes]
rs59837747	1.00[EUR][1000 genomes]
rs60500053	1.00[EUR][1000 genomes]
rs61491150	1.00[EUR][1000 genomes]
rs634639	0.99[ASN][1000 genomes]
rs649269	0.99[ASN][1000 genomes]
rs6668295	1.00[EUR][1000 genomes]
rs72480203	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525198	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3424702	chr1:153015726-153032343	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv946394	chr1:153017705-153029390	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153018000-153019800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:153018000-153019800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links