Variant report

Variant	rs9879239
Chromosome Location	chr3:113282129-113282130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113282001..113285140-chr3:113291116..113294259,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11929640	0.85[AMR][1000 genomes]
rs12631929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1567781	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2048624	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28446408	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28530478	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28564696	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34842926	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3896909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3932276	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41271363	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560271	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4560272	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682493	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682494	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55941419	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56721892	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62265514	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265515	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265518	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62265519	0.85[AMR][1000 genomes]
rs62265520	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62265521	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787428	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72950888	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7637206	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816095	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823358	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9844542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854140	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9868243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874993	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9985452	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113257200-113283400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:113276800-113284800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:113276800-113294200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:113277600-113283200	Weak transcription	GM12878-XiMat	blood
5	chr3:113277600-113285600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:113278200-113285200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:113279200-113300000	Weak transcription	Thymus	Thymus
8	chr3:113279600-113283200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:113279800-113282200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:113280000-113286400	Weak transcription	Fetal Thymus	thymus
11	chr3:113280200-113286400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:113280200-113299200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:113280400-113304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:113280600-113302400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
17	chr3:113280800-113285600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:113281000-113283000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:113281000-113285600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:113281000-113286000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:113281000-113286400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:113281000-113286400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:113281200-113285000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:113281200-113286600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:113281400-113302200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:113281600-113282200	Enhancers	HMEC	breast
27	chr3:113281600-113284800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:113281600-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:113281600-113296400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:113281800-113282200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:113281800-113296200	Strong transcription	Primary T cells from cord blood	blood
32	chr3:113282000-113285200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links