Variant report

Variant	rs12901649
Chromosome Location	chr15:73469535-73469536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1017808	0.84[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs11072405	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072407	0.89[ASN][1000 genomes]
rs11072408	0.88[ASN][1000 genomes]
rs11072411	0.80[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs11072412	0.80[ASN][1000 genomes]
rs1119251	0.84[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs11634045	0.89[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs11636981	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs11856537	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs12439852	0.81[ASN][1000 genomes]
rs12594776	0.84[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs12595434	0.85[CHB][hapmap]
rs12901272	0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12912737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382782	0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs1564347	0.90[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs1585766	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16957683	0.81[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs1878940	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1904335	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2061890	0.92[ASN][1000 genomes]
rs2415142	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415145	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2415146	0.88[ASN][1000 genomes]
rs28742992	0.87[ASN][1000 genomes]
rs34456824	0.81[ASN][1000 genomes]
rs34953385	0.90[ASN][1000 genomes]
rs35348961	0.88[ASN][1000 genomes]
rs35391014	0.92[ASN][1000 genomes]
rs35608416	0.89[ASN][1000 genomes]
rs35778649	0.81[ASN][1000 genomes]
rs36072085	0.94[ASN][1000 genomes]
rs3784795	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4776623	0.81[ASN][1000 genomes]
rs4776631	0.82[ASN][1000 genomes]
rs4777585	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4777587	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs4777588	0.87[ASN][1000 genomes]
rs4777592	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs486267	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs488156	0.82[GIH][hapmap]
rs498005	0.82[GIH][hapmap]
rs520824	0.82[ASN][1000 genomes]
rs549253	0.82[ASN][1000 genomes]
rs559260	0.80[ASN][1000 genomes]
rs563076	0.81[ASN][1000 genomes]
rs59628124	0.94[ASN][1000 genomes]
rs6495046	0.81[ASN][1000 genomes]
rs6495050	0.82[ASN][1000 genomes]
rs6495051	0.83[ASN][1000 genomes]
rs6495052	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs6495053	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs6495057	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs6495058	0.89[ASN][1000 genomes]
rs7168555	0.88[ASN][1000 genomes]
rs7177758	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7184025	0.86[ASN][1000 genomes]
rs7495084	0.87[ASN][1000 genomes]
rs8039418	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043494	0.86[ASN][1000 genomes]
rs983067	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73447200-73470000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:73450000-73475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:73450000-73477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:73452200-73470000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:73454800-73471600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:73455000-73473800	Weak transcription	Fetal Stomach	stomach
9	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:73457600-73470600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:73458600-73473200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:73458600-73478000	Weak transcription	Colonic Mucosa	Colon
13	chr15:73459000-73470000	Weak transcription	Liver	Liver
14	chr15:73459000-73470400	Weak transcription	Fetal Lung	lung
15	chr15:73459000-73470600	Weak transcription	Fetal Kidney	kidney
16	chr15:73459000-73472400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:73459000-73482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:73459200-73471600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:73459200-73473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:73459200-73473800	Weak transcription	Fetal Intestine Small	intestine
21	chr15:73459400-73473400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:73460800-73472400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:73462400-73473800	Weak transcription	Fetal Brain Female	brain
24	chr15:73466200-73473800	Weak transcription	Esophagus	oesophagus
25	chr15:73466800-73470600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:73466800-73471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:73466800-73471800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:73466800-73473800	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:73466800-73482000	Weak transcription	Psoas Muscle	Psoas
30	chr15:73467000-73473800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:73467000-73473800	Weak transcription	Aorta	Aorta
32	chr15:73467000-73473800	Weak transcription	Gastric	stomach
33	chr15:73467200-73473800	Weak transcription	Pancreas	Pancrea
34	chr15:73467400-73473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:73467600-73473200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:73467600-73473800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:73467800-73475200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:73467800-73476800	Weak transcription	Fetal Brain Male	brain
39	chr15:73468000-73470000	Weak transcription	Brain Angular Gyrus	brain
40	chr15:73468000-73475400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:73468200-73472600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:73468200-73473600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:73468200-73473800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:73468200-73475000	Weak transcription	Brain Substantia Nigra	brain
45	chr15:73468400-73475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:73468400-73475600	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:73468600-73471400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:73468600-73476200	Weak transcription	Small Intestine	intestine
49	chr15:73468600-73481200	Weak transcription	Lung	lung
50	chr15:73468800-73469600	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links