Variant report

Variant	rs16962490
Chromosome Location	chr15:49743628-49743629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10047970	0.86[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10083602	0.83[EUR][1000 genomes]
rs10519230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057638	0.81[EUR][1000 genomes]
rs11070692	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs11070693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070694	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070696	0.81[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11630629	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11631040	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631687	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632674	0.86[CEU][hapmap]
rs11634751	0.86[CEU][hapmap]
rs11636378	0.81[CEU][hapmap]
rs11636671	0.86[ASN][1000 genomes]
rs11636795	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852524	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs12437460	0.81[EUR][1000 genomes]
rs12438444	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12438856	0.83[EUR][1000 genomes]
rs12439479	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440323	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441004	0.81[AMR][1000 genomes]
rs12441304	0.86[CEU][hapmap]
rs12442143	0.83[EUR][1000 genomes]
rs12900001	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913745	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1429556	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1532955	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1588130	0.86[CEU][hapmap]
rs1605481	0.86[CEU][hapmap]
rs16962243	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs16962486	0.94[AFR][1000 genomes]
rs16962528	0.83[EUR][1000 genomes]
rs16973952	0.83[EUR][1000 genomes]
rs17401417	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1874615	0.86[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1904317	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs1911614	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs2413942	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2413946	0.83[EUR][1000 genomes]
rs2413953	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2413954	0.86[CEU][hapmap]
rs2413957	0.81[EUR][1000 genomes]
rs2413959	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs28460471	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2899433	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4303431	0.86[CEU][hapmap]
rs4316697	1.00[ASW][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs4321137	0.81[EUR][1000 genomes]
rs4350524	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs4614670	0.83[EUR][1000 genomes]
rs4775811	0.81[EUR][1000 genomes]
rs4775814	0.86[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs4775815	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs57186766	0.81[EUR][1000 genomes]
rs58284238	0.81[EUR][1000 genomes]
rs58410445	0.83[EUR][1000 genomes]
rs6493364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6493369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493371	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6493376	0.86[CEU][hapmap]
rs7162800	0.83[MEX][hapmap]
rs7166049	0.83[EUR][1000 genomes]
rs7166202	0.86[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7166498	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7167041	0.86[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7167429	0.86[CEU][hapmap]
rs7170426	0.86[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7178143	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7178468	0.86[CEU][hapmap]
rs733097	0.86[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs8026236	0.83[EUR][1000 genomes]
rs8031892	0.85[AFR][1000 genomes]
rs8032650	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap]
rs8035468	0.86[CEU][hapmap]
rs8039062	0.81[EUR][1000 genomes]
rs8041781	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs9302148	0.80[EUR][1000 genomes]
rs965134	0.86[CEU][hapmap]
rs9920772	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9972329	0.86[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9972429	0.83[EUR][1000 genomes]
rs9972565	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv526246	chr15:49738233-49749735	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16962490	DTWD1	cis	cerebellum	SCAN
rs16962490	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs16962490	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49730400-49744600	Weak transcription	NHLF	lung
2	chr15:49732000-49750200	Weak transcription	HSMM	muscle
3	chr15:49737000-49751200	Weak transcription	Ovary	ovary
4	chr15:49737600-49744200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:49739200-49744200	Weak transcription	NHDF-Ad	bronchial
6	chr15:49741800-49747400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:49742000-49752000	Weak transcription	Adipose Nuclei	Adipose
8	chr15:49742800-49748000	Weak transcription	Fetal Heart	heart
9	chr15:49742800-49750400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:49743000-49744600	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:49743000-49744600	Weak transcription	Osteobl	bone
12	chr15:49743000-49745600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:49743000-49748000	Weak transcription	Fetal Lung	lung
14	chr15:49743200-49744400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:49743200-49745800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:49743200-49747200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:49743200-49748400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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