Variant report

Variant	rs12440299
Chromosome Location	chr15:72376841-72376842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11072341	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072344	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1120002	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856068	0.81[EUR][1000 genomes]
rs12437582	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439689	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441470	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441567	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441622	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442680	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12443127	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592615	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592806	0.86[EUR][1000 genomes]
rs12592858	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592932	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592969	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12593857	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593946	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1426168	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1471688	0.81[EUR][1000 genomes]
rs1545825	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16953747	0.81[EUR][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956539	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16956599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16956602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1905337	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979459	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288256	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2291279	0.90[EUR][1000 genomes]
rs2305705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2306575	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2415129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28397923	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28639924	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28653163	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28701834	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899774	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929514	0.86[ASN][1000 genomes]
rs2929515	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929521	0.92[ASN][1000 genomes]
rs2929522	0.92[ASN][1000 genomes]
rs2929524	0.86[ASN][1000 genomes]
rs2929530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929531	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2929533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957369	0.92[ASN][1000 genomes]
rs2957729	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957730	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957733	0.85[ASN][1000 genomes]
rs2957741	0.92[ASN][1000 genomes]
rs2957747	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2957748	0.84[ASN][1000 genomes]
rs2957749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34625473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35696756	0.81[EUR][1000 genomes]
rs35773391	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3809505	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825869	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4511484	0.92[ASN][1000 genomes]
rs4776583	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777472	0.80[ASN][1000 genomes]
rs4777479	0.81[ASN][1000 genomes]
rs6494976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7161909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7162134	0.81[ASN][1000 genomes]
rs7162931	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7164646	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7168999	1.00[YRI][hapmap]
rs7171446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177067	0.84[AFR][1000 genomes]
rs7178613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7178876	0.87[AFR][1000 genomes]
rs8026894	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs8029218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs8034436	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8034722	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8182066	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8192381	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs981695	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920148	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
2	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
6	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
8	esv11550	chr15:72353301-72395288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv904337	chr15:72361942-72390515	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv869747	chr15:72372245-72403103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
12	nsv510665	chr15:72374862-72407548	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72351200-72395800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:72353600-72379600	Weak transcription	Primary T cells from cord blood	blood
3	chr15:72354000-72378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:72361600-72377400	Weak transcription	Fetal Intestine Small	intestine
5	chr15:72361600-72390600	Weak transcription	Aorta	Aorta
6	chr15:72361600-72391400	Weak transcription	Ovary	ovary
7	chr15:72367200-72407600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:72367800-72377400	Weak transcription	Fetal Stomach	stomach
9	chr15:72370000-72378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:72370800-72378600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:72371200-72377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:72371400-72379600	Weak transcription	Brain Anterior Caudate	brain
13	chr15:72372200-72378000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:72372200-72399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:72373600-72378400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:72373600-72394400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:72375000-72379400	Weak transcription	Right Ventricle	heart
18	chr15:72375000-72408200	Weak transcription	Primary B cells from cord blood	blood
19	chr15:72375200-72378800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:72375400-72377800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:72375400-72378400	Weak transcription	Psoas Muscle	Psoas
22	chr15:72375800-72395600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:72376200-72377000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:72376400-72378400	Weak transcription	Esophagus	oesophagus
25	chr15:72376400-72381400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:72376600-72377000	Strong transcription	Fetal Lung	lung
27	chr15:72376800-72377000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr15:72376800-72377200	ZNF genes & repeats	Fetal Brain Female	brain
29	chr15:72376800-72379000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:72376800-72379200	Enhancers	HSMMtube	muscle

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