Variant report

Variant	rs2413958
Chromosome Location	chr15:49760546-49760547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49759384..49762245-chr15:49912531..49914153,2	MCF-7	breast:
2	chr15:49760434..49762831-chr15:49768683..49770217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10048065	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519233	0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1055254	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070698	0.86[YRI][hapmap]
rs11070707	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070711	0.82[YRI][hapmap]
rs12901416	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12902107	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12902794	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13329455	0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1354918	0.83[EUR][1000 genomes]
rs1354919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1354920	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs1395900	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546424	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1546425	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1580996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1580997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1588127	0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs16962235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962237	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962238	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962256	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962257	1.00[CHB][hapmap]
rs16962259	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962262	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962274	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962308	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962331	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962416	1.00[CHB][hapmap]
rs17476940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17480434	0.85[EUR][1000 genomes]
rs1814711	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1874614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874615	0.82[LWK][hapmap]
rs1874616	0.82[LWK][hapmap];0.83[MKK][hapmap]
rs1911614	0.81[LWK][hapmap]
rs2059935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2078024	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2127243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2169931	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413947	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413953	0.82[LWK][hapmap]
rs2413963	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28393768	0.86[EUR][1000 genomes]
rs28408092	0.85[EUR][1000 genomes]
rs28409376	0.82[EUR][1000 genomes]
rs28430272	0.86[EUR][1000 genomes]
rs28465200	0.83[EUR][1000 genomes]
rs28484276	0.85[EUR][1000 genomes]
rs28492008	0.84[EUR][1000 genomes]
rs28635979	0.82[EUR][1000 genomes]
rs28669217	0.85[EUR][1000 genomes]
rs28798135	0.81[EUR][1000 genomes]
rs28843724	0.81[EUR][1000 genomes]
rs2899437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3210227	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4362337	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs4396481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774539	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs6493371	0.82[LWK][hapmap]
rs7167625	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs733097	0.82[LWK][hapmap]
rs8029506	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8031680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8034473	0.82[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8038373	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040436	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs8040716	0.85[EUR][1000 genomes]
rs967892	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs967893	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9920574	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv974574	chr15:49752716-49764974	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1043119	chr15:49760222-49844366	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413958	DTWD1	cis	cerebellum	SCAN
rs2413958	TRPM7	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49752400-49764000	Weak transcription	HSMM	muscle
2	chr15:49755000-49764000	Weak transcription	Fetal Lung	lung
3	chr15:49755400-49764200	Weak transcription	Fetal Heart	heart
4	chr15:49757800-49760800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:49758000-49761000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:49758200-49761200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:49758200-49761200	Enhancers	Colon Smooth Muscle	Colon
8	chr15:49758200-49761600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:49758400-49761200	Enhancers	Hela-S3	cervix
10	chr15:49759400-49760600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:49759400-49761200	Enhancers	NHLF	lung
12	chr15:49759600-49760600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:49759600-49761000	Enhancers	Adipose Nuclei	Adipose
14	chr15:49759600-49761200	Enhancers	Liver	Liver
15	chr15:49759600-49762800	Weak transcription	GM12878-XiMat	blood
16	chr15:49759600-49763800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:49759800-49760600	Enhancers	Osteobl	bone
18	chr15:49759800-49761200	Enhancers	Rectal Smooth Muscle	rectum
19	chr15:49760000-49760600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:49760200-49760600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:49760400-49760800	Flanking Active TSS	NHDF-Ad	bronchial
22	chr15:49760400-49761200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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