Variant report

Variant	rs2339501
Chromosome Location	chr1:153013948-153013949
allele	C/T
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	JUN	chr1:153013532-153014063	K562	blood:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013548-153013556 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
2	EP300	chr1:153013556-153014116	K562	blood:	n/a	n/a
3	FOS	chr1:153013607-153014058	MCF10A-Er-Src	breast:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
4	FOS	chr1:153013643-153014033	MCF10A-Er-Src	breast:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
5	TEAD4	chr1:153013391-153014017	K562	blood:	n/a	n/a
6	MYC	chr1:153013595-153014010	K562	blood:	n/a	chr1:153013921-153013930 chr1:153013784-153013793
7	STAT3	chr1:153013625-153013967	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:153013694-153013965	MCF10A-Er-Src	breast:	n/a	n/a
9	JUN	chr1:153013666-153013964	K562	blood:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
10	CEBPB	chr1:153013681-153013964	K562	blood:	n/a	n/a
11	MAZ	chr1:153013495-153013977	K562	blood:	n/a	chr1:153013921-153013930 chr1:153013784-153013793
12	FOS	chr1:153013545-153014108	MCF10A-Er-Src	breast:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013548-153013556 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
13	JUND	chr1:153013497-153014094	K562	blood:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013548-153013556 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
14	JUN	chr1:153012837-153014143	K562	blood:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013548-153013556 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
15	RCOR1	chr1:153013509-153014025	K562	blood:	n/a	n/a
16	CUX1	chr1:153013518-153013964	K562	blood:	n/a	n/a
17	MYC	chr1:153013770-153013956	MCF10A-Er-Src	breast:	n/a	chr1:153013921-153013930 chr1:153013784-153013793
18	FOS	chr1:153013607-153014112	MCF10A-Er-Src	breast:	n/a	chr1:153013923-153013930 chr1:153013922-153013930 chr1:153013922-153013930 chr1:153013785-153013794 chr1:153013784-153013795 chr1:153013918-153013929
19	MAFK	chr1:153013683-153014222	K562	blood:	n/a	n/a
20	ATF1	chr1:153013641-153013966	K562	blood:	n/a	n/a

Variant related genes	Relation type
SPRR2D	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10157591	1.00[CEU][hapmap]
rs10494288	1.00[EUR][1000 genomes]
rs10888521	1.00[EUR][1000 genomes]
rs11205130	1.00[EUR][1000 genomes]
rs11205131	1.00[CEU][hapmap]
rs11205147	1.00[EUR][1000 genomes]
rs11205183	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11806470	1.00[EUR][1000 genomes]
rs12021601	1.00[CEU][hapmap]
rs12022870	1.00[CEU][hapmap]
rs12024694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026519	1.00[CEU][hapmap]
rs12029192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12032522	1.00[EUR][1000 genomes]
rs12036590	1.00[CEU][hapmap]
rs12036697	1.00[EUR][1000 genomes]
rs12037255	1.00[CEU][hapmap]
rs12037754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12046394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12047099	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047187	0.99[ASN][1000 genomes]
rs12047225	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs12239808	1.00[CEU][hapmap]
rs12239812	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12239814	1.00[CEU][hapmap]
rs1415973	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs167452	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16834734	1.00[CEU][hapmap]
rs16834746	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834751	1.00[CEU][hapmap]
rs16834838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs16834871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1846857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1890284	0.83[CHB][hapmap]
rs1974141	1.00[EUR][1000 genomes]
rs1995307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339383	1.00[CEU][hapmap]
rs28647391	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879485	1.00[CEU][hapmap]
rs310096	0.92[ASN][1000 genomes]
rs310097	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs310098	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs310099	0.92[ASN][1000 genomes]
rs310101	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs310104	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs310112	0.83[ASN][1000 genomes]
rs310113	0.84[ASN][1000 genomes]
rs310116	0.84[ASN][1000 genomes]
rs310117	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs310125	1.00[ASN][1000 genomes]
rs36090881	1.00[EUR][1000 genomes]
rs367220	0.90[ASN][1000 genomes]
rs373451	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3737862	1.00[CEU][hapmap]
rs374170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs377182	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3856020	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399274	0.90[ASN][1000 genomes]
rs4041337	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4041340	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs418550	0.87[CHB][hapmap]
rs423692	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4240863	1.00[CEU][hapmap]
rs4240864	1.00[EUR][1000 genomes]
rs442209	0.91[ASN][1000 genomes]
rs454186	0.87[CHB][hapmap]
rs4845328	1.00[EUR][1000 genomes]
rs4845498	1.00[EUR][1000 genomes]
rs57583857	0.83[AFR][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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6668295	1.00[EUR][1000 genomes]
rs72480203	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74132206	0.83[AFR][1000 genomes]
rs74132527	0.83[AFR][1000 genomes]
rs7525198	0.92[ASN][1000 genomes]
rs7532449	1.00[CEU][hapmap]
rs7552416	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv947197	chr1:153006138-153017705	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153013000-153015800	Enhancers	K562	blood
2	chr1:153013200-153014400	Enhancers	NHEK	skin
3	chr1:153013400-153014000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:153013400-153014400	Enhancers	HMEC	breast
5	chr1:153013400-153015800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:153013600-153014600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:153013800-153014000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:153013800-153014200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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