Variant report

Variant	rs3935253
Chromosome Location	chr3:23999756-23999757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23958189..23961331-chr3:23997888..24001108,3	MCF-7	breast:
2	chr3:23955851..23960188-chr3:23998337..24001245,6	K562	blood:
3	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:
5	chr3:23995729..23998048-chr3:23998292..24000934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10084748	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11129128	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129130	0.82[YRI][hapmap]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13321439	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13321440	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533141	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1567579	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34866549	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35755171	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.85[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6776568	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6778577	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790140	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71324126	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72627094	0.82[AMR][1000 genomes]
rs73150266	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7611018	1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs954748	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs9812870	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9817923	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9853954	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs9863176	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883834	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
2	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
5	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
7	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
8	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
13	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
14	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
16	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:23992000-24000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:23992000-24001600	Weak transcription	Fetal Stomach	stomach
20	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
21	chr3:23992200-24000200	Weak transcription	HMEC	breast
22	chr3:23992200-24000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:23992200-24001200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:23992200-24001400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:23992400-24002400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:23992400-24003400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:23992400-24003400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:23992400-24003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:23993600-24000200	Weak transcription	NHEK	skin
31	chr3:23993600-24000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:23993600-24009400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
34	chr3:23993800-24001000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:23995200-24003200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:23995200-24003200	Weak transcription	Dnd41	blood
38	chr3:23995200-24003400	Weak transcription	GM12878-XiMat	blood
39	chr3:23995600-24000800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:23995600-24001000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:23995600-24003200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:23995800-23999800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:23995800-24000800	Weak transcription	Primary B cells from cord blood	blood
44	chr3:23995800-24000800	Weak transcription	Fetal Heart	heart
45	chr3:23995800-24000800	Weak transcription	K562	blood
46	chr3:23995800-24003000	Weak transcription	HepG2	liver
47	chr3:23996000-23999800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:23996000-24000400	Weak transcription	Aorta	Aorta
49	chr3:23996000-24001200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:23996000-24012600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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