Variant report

Variant	rs2599471
Chromosome Location	chr19:43949253-43949254
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:43947823..43950572-chr19:43967998..43969717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124466	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12974736	0.84[ASN][1000 genomes]
rs12976910	0.85[ASN][1000 genomes]
rs12976959	0.85[ASN][1000 genomes]
rs12977973	0.85[ASN][1000 genomes]
rs12978127	0.85[ASN][1000 genomes]
rs12978525	0.85[ASN][1000 genomes]
rs12978874	0.85[ASN][1000 genomes]
rs12979480	0.85[ASN][1000 genomes]
rs12980013	0.85[ASN][1000 genomes]
rs12980224	0.85[ASN][1000 genomes]
rs12983123	0.83[ASN][1000 genomes]
rs12984388	0.85[ASN][1000 genomes]
rs12984476	0.85[ASN][1000 genomes]
rs12984674	0.85[ASN][1000 genomes]
rs2247798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2599472	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2599474	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2599475	0.94[ASN][1000 genomes]
rs2682596	0.82[AMR][1000 genomes]
rs2682597	0.84[ASN][1000 genomes]
rs2682598	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34228745	0.85[ASN][1000 genomes]
rs34860326	0.85[ASN][1000 genomes]
rs34865699	0.85[ASN][1000 genomes]
rs35132532	0.85[ASN][1000 genomes]
rs35146204	0.85[ASN][1000 genomes]
rs35519460	0.84[ASN][1000 genomes]
rs35566664	0.84[ASN][1000 genomes]
rs35573924	0.84[ASN][1000 genomes]
rs35585729	0.85[ASN][1000 genomes]
rs35895695	0.85[ASN][1000 genomes]
rs36049523	0.85[ASN][1000 genomes]
rs3859443	0.83[ASN][1000 genomes]
rs3859444	0.85[ASN][1000 genomes]
rs4464191	0.85[ASN][1000 genomes]
rs4803630	0.85[ASN][1000 genomes]
rs60765266	0.85[ASN][1000 genomes]
rs71350679	0.84[ASN][1000 genomes]
rs71350682	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1060280	chr19:43866823-43959685	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv520852	chr19:43885085-43960114	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv579850	chr19:43885085-43960114	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1066231	chr19:43918840-43954915	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv579851	chr19:43920612-43955114	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv1061862	chr19:43925290-43954915	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv1058848	chr19:43925290-43957387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43943200-43953800	Weak transcription	Right Atrium	heart
2	chr19:43943400-43951400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:43943800-43954800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:43944000-43951000	Weak transcription	Esophagus	oesophagus
5	chr19:43944000-43956600	Weak transcription	Spleen	Spleen
6	chr19:43944200-43951000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:43944200-43954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:43944200-43954800	Weak transcription	Fetal Thymus	thymus
9	chr19:43944400-43951000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr19:43944400-43951200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:43944800-43951000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:43944800-43951000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:43945000-43951000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:43945000-43951000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr19:43947800-43949400	Enhancers	Placenta	Placenta
16	chr19:43947800-43949600	Enhancers	Primary T cells from cord blood	blood
17	chr19:43948400-43950400	Enhancers	K562	blood
18	chr19:43948800-43950200	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr19:43948800-43951800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr19:43949000-43949400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr19:43949000-43949400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:43949000-43949600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr19:43949000-43949800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:43949000-43950000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr19:43949200-43949800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:43949200-43951400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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