Variant report

Variant	rs12653772
Chromosome Location	chr5:49970496-49970497
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	chr20:9344139..9345018-chr5:49970141..49970936,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10471414	0.85[JPT][hapmap]
rs10512906	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737958	0.85[JPT][hapmap]
rs1125916	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747930	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11950328	0.91[ASN][1000 genomes]
rs11954386	0.85[JPT][hapmap]
rs12055210	0.85[JPT][hapmap]
rs12654329	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654399	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12659764	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13159505	0.89[ASN][1000 genomes]
rs13162945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13166556	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180000	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13186089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs166863	0.85[JPT][hapmap]
rs16877029	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16885842	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16886818	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1862547	0.88[EUR][1000 genomes]
rs1993955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs204915	0.90[JPT][hapmap]
rs2404958	0.85[JPT][hapmap]
rs2463797	0.85[JPT][hapmap]
rs26072	0.85[JPT][hapmap]
rs27255	0.85[JPT][hapmap]
rs27598	0.81[JPT][hapmap]
rs27934	0.85[JPT][hapmap]
rs282544	0.95[JPT][hapmap]
rs282556	0.81[JPT][hapmap]
rs32396	0.85[JPT][hapmap]
rs34241669	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34389644	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34428476	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34674487	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35328303	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35571312	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3806889	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4548483	0.85[JPT][hapmap]
rs61479216	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62365481	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62365519	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62366945	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368285	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450384	0.85[JPT][hapmap]
rs67151831	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7700817	0.84[MEX][hapmap]
rs7723602	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv968910	chr5:49961360-49980983	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv980791	chr5:49968246-49975820	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12653772	PARP8	cis	Esophagus Muscularis	GTEx
rs12653772	PARP8	cis	lung	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49964400-49975400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:49964400-49977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:49964400-49982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:49964400-49983400	Weak transcription	Esophagus	oesophagus
5	chr5:49964800-49970800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:49964800-49976200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:49964800-49976600	Weak transcription	NHDF-Ad	bronchial
8	chr5:49964800-49977600	Weak transcription	Brain Anterior Caudate	brain
9	chr5:49964800-49977800	Weak transcription	Fetal Brain Male	brain
10	chr5:49965600-49976400	Weak transcription	HMEC	breast
11	chr5:49965800-49973400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr5:49965800-49973800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:49965800-49976000	Weak transcription	Fetal Lung	lung
14	chr5:49965800-49976000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:49965800-49982000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:49965800-49983600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:49966000-49975400	Weak transcription	NHEK	skin
18	chr5:49968000-49970600	Enhancers	Primary B cells from peripheral blood	blood
19	chr5:49968400-49970600	Enhancers	Dnd41	blood
20	chr5:49968400-49971600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:49968400-49972000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:49968400-49972800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:49968400-49974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:49968400-49977600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:49968600-49970600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:49968600-49971400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr5:49968600-49971600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr5:49968600-49976000	Weak transcription	Fetal Stomach	stomach
29	chr5:49968800-49970600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr5:49968800-49974600	Weak transcription	Spleen	Spleen
31	chr5:49968800-49975600	Weak transcription	Primary B cells from cord blood	blood
32	chr5:49968800-49990400	Weak transcription	Small Intestine	intestine
33	chr5:49969000-49971800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:49969000-49980400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:49969400-49970600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr5:49969400-49970800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:49969400-49974400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:49969800-49970800	Flanking Active TSS	GM12878-XiMat	blood
39	chr5:49969800-49972200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:49970000-49970600	Enhancers	Aorta	Aorta
41	chr5:49970200-49970600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:49970200-49971600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr5:49970200-49972000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:49970200-49972000	Weak transcription	Primary T cells from cord blood	blood
45	chr5:49970200-49973200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:49970200-49974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:49970200-49974400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr5:49970200-49977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:49970400-49970600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:49970400-49970800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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