Variant report

Variant	rs1259311
Chromosome Location	chr3:120176818-120176819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120176725..120179691-chr3:120180147..120181932,2	K562	blood:
2	chr3:120135734..120138028-chr3:120174472..120177330,2	MCF-7	breast:
3	chr3:120169359..120172197-chr3:120175284..120177475,2	K562	blood:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1123897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1123898	0.98[ASN][1000 genomes]
rs1147706	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1147710	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1147717	0.83[ASN][1000 genomes]
rs1147720	0.88[CHB][hapmap]
rs1259318	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs1259329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259333	0.86[JPT][hapmap]
rs1259334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259335	0.85[JPT][hapmap]
rs1259336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259339	0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1259457	0.83[ASN][1000 genomes]
rs1259471	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259473	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1267675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1270209	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520881	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1716837	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes]
rs1733298	0.93[EUR][1000 genomes]
rs1733299	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1733301	0.93[EUR][1000 genomes]
rs1733303	0.93[EUR][1000 genomes]
rs1733304	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733307	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982186	0.83[ASN][1000 genomes]
rs2252084	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2700263	0.92[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5000757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs735138	0.83[EUR][1000 genomes]
rs874477	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs874478	0.95[EUR][1000 genomes]
rs874479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[EUR][1000 genomes]
rs874480	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9631455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120170400-120190800	Weak transcription	Aorta	Aorta
2	chr3:120170600-120178000	Weak transcription	Left Ventricle	heart
3	chr3:120170600-120178800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:120170800-120178200	Weak transcription	Right Atrium	heart
5	chr3:120171000-120179600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:120171400-120179400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:120171800-120180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:120173600-120177200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:120173600-120179200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:120174600-120177200	Weak transcription	Rectal Mucosa Donor 31	rectum

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