Variant report

Variant	rs1382444
Chromosome Location	chr15:39870458-39870459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39869407..39871427-chr15:39874178..39876262,2	K562	blood:
2	chr15:39869319..39871177-chr15:39871544..39874678,3	MCF-7	breast:
3	chr15:39867115..39869175-chr15:39869428..39872036,2	MCF-7	breast:
4	chr15:39869641..39872520-chr15:39877889..39880142,2	K562	blood:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10152903	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs10152951	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1038097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051442	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10520146	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12438058	1.00[ASN][1000 genomes]
rs12442155	1.00[ASN][1000 genomes]
rs12442221	1.00[ASN][1000 genomes]
rs1382443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16969487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16969491	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16969547	1.00[CHB][hapmap]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17631807	1.00[ASN][1000 genomes]
rs17632916	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702987	1.00[ASN][1000 genomes]
rs17705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17706179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813493	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988082	0.87[EUR][1000 genomes]
rs1988555	0.90[EUR][1000 genomes]
rs1994380	1.00[CHB][hapmap]
rs2129457	1.00[CHB][hapmap]
rs2228262	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2228263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2618156	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618160	0.97[EUR][1000 genomes]
rs2618161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618164	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes]
rs2618165	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664123	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664136	0.96[EUR][1000 genomes]
rs2664137	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs2664140	0.97[EUR][1000 genomes]
rs2664142	0.97[EUR][1000 genomes]
rs28377784	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28549326	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28619289	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28622135	1.00[ASN][1000 genomes]
rs28653011	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34878675	0.84[EUR][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319740	0.83[CEU][hapmap]
rs4415979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4503768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs45461294	0.94[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58188999	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59578395	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59628570	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	1.00[ASN][1000 genomes]
rs62002378	1.00[ASN][1000 genomes]
rs62002379	1.00[ASN][1000 genomes]
rs62002380	1.00[ASN][1000 genomes]
rs62002384	1.00[ASN][1000 genomes]
rs6492905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs74008526	1.00[ASN][1000 genomes]
rs74008647	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008648	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.90[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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1382444	CASC5	cis	parietal	SCAN
rs1382444	CHD4	trans	parietal	SCAN
rs1382444	WNT11	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39851000-39871800	Weak transcription	Pancreas	Pancrea
2	chr15:39854400-39870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39857800-39870600	Weak transcription	HSMMtube	muscle
4	chr15:39863600-39871200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:39865800-39871200	Weak transcription	Esophagus	oesophagus
6	chr15:39866000-39871000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:39866000-39871200	Weak transcription	Adipose Nuclei	Adipose
8	chr15:39866400-39870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:39866400-39870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:39866400-39870800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:39866600-39870800	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:39866800-39871200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:39867000-39870600	Weak transcription	HMEC	breast
14	chr15:39867000-39870600	Weak transcription	NHDF-Ad	bronchial
15	chr15:39867000-39870600	Weak transcription	Osteobl	bone
16	chr15:39867400-39870800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:39867600-39871000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:39869600-39871200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:39869600-39871400	Enhancers	HSMM	muscle
20	chr15:39870000-39871600	Enhancers	Fetal Lung	lung
21	chr15:39870400-39871200	Enhancers	HUVEC	blood vessel
22	chr15:39870400-39871600	Enhancers	Fetal Stomach	stomach

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