Variant report

Variant	rs1854176
Chromosome Location	chr13:30333262-30333263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1058650	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12872400	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1323931	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1410110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1927193	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2182129	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2234416	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2388246	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2388247	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2761938	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2761939	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2761940	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278034	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2892463	0.87[ASW][hapmap];0.81[GIH][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs4083610	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4769772	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4769775	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6490429	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6490430	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72623487	0.89[ASN][1000 genomes]
rs7326253	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7330356	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7331353	0.91[AFR][1000 genomes]
rs7335148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7342470	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9314972	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314973	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314974	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314975	0.90[ASN][1000 genomes]
rs9506226	0.80[ASN][1000 genomes]
rs9506229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9506231	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9508550	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508553	0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs9508554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9508558	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs9508568	0.81[ASN][1000 genomes]
rs9550494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9551739	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9551741	0.86[ASN][1000 genomes]
rs9551744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9551751	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9551753	0.81[CHB][hapmap]
rs9578136	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9578139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription 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

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30317600-30335800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:30324600-30340400	Weak transcription	Adipose Nuclei	Adipose
3	chr13:30326600-30343200	Weak transcription	Spleen	Spleen
4	chr13:30328400-30337200	Weak transcription	Osteobl	bone
5	chr13:30328400-30340600	Weak transcription	NHLF	lung
6	chr13:30328600-30337200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:30328600-30341200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:30328800-30337200	Weak transcription	NHDF-Ad	bronchial
9	chr13:30328800-30337400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr13:30328800-30340400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:30328800-30340400	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:30328800-30340800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr13:30328800-30347800	Weak transcription	Fetal Kidney	kidney
14	chr13:30328800-30351800	Weak transcription	NH-A	brain
15	chr13:30328800-30352600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:30329000-30335800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:30329200-30335400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr13:30329200-30338000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr13:30329200-30340000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:30329200-30340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:30329200-30351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:30330600-30355000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:30332200-30333800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:30332200-30336200	Weak transcription	HSMMtube	muscle
25	chr13:30332400-30334000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:30332600-30333600	Enhancers	Primary B cells from cord blood	blood
27	chr13:30332600-30333800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr13:30332800-30333400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:30332800-30333400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr13:30332800-30333400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:30332800-30333400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr13:30332800-30333400	Active TSS	Duodenum Mucosa	Duodenum
33	chr13:30332800-30333400	Enhancers	Placenta	Placenta
34	chr13:30332800-30333400	Active TSS	HepG2	liver
35	chr13:30332800-30333600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr13:30332800-30333600	Enhancers	Primary hematopoietic stem cells	blood
37	chr13:30332800-30333600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr13:30332800-30333600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr13:30332800-30333600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:30332800-30333800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr13:30332800-30333800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:30332800-30336400	Enhancers	Primary B cells from peripheral blood	blood
43	chr13:30333000-30333400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:30333000-30333400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr13:30333000-30340600	Weak transcription	Fetal Thymus	thymus
46	chr13:30333000-30340600	Weak transcription	Thymus	Thymus
47	chr13:30333200-30333400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr13:30333200-30333600	Flanking Active TSS	GM12878-XiMat	blood
49	chr13:30333200-30335400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:30333200-30338000	Weak transcription	Rectal Mucosa Donor 31	rectum

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