Variant report

Variant	rs11858160
Chromosome Location	chr15:50428495-50428496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50428036..50430534-chr15:50437642..50439457,2	MCF-7	breast:
2	chr15:50420970..50423759-chr15:50428011..50430538,2	MCF-7	breast:
3	chr15:50418543..50420300-chr15:50426585..50429061,2	MCF-7	breast:
4	chr15:50425943..50428562-chr15:50428956..50430506,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10519258	0.83[GIH][hapmap]
rs10519263	0.82[MEX][hapmap]
rs11070744	0.83[GIH][hapmap]
rs11070746	0.83[GIH][hapmap]
rs11070756	1.00[ASN][1000 genomes]
rs11070757	1.00[ASN][1000 genomes]
rs11853146	0.83[GIH][hapmap]
rs11854761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854881	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12906623	0.96[ASN][1000 genomes]
rs12912519	0.96[ASN][1000 genomes]
rs16963416	0.82[MEX][hapmap]
rs16963420	0.82[MEX][hapmap]
rs16963439	0.82[MEX][hapmap]
rs16963441	0.82[MEX][hapmap]
rs17415862	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17499726	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414009	0.83[GIH][hapmap]
rs2414037	0.80[AMR][1000 genomes]
rs34490804	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803371	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55740521	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55852503	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55853214	0.88[ASN][1000 genomes]
rs55970302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083537	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56307748	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57335604	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58277329	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59690694	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60383354	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60387657	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493395	0.83[GIH][hapmap]
rs66472276	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7163415	0.83[GIH][hapmap]
rs7175274	0.82[MEX][hapmap]
rs72737004	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72737014	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737020	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737025	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737026	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737028	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737030	1.00[ASN][1000 genomes]
rs72737033	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737034	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737035	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737040	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72737046	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72737047	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72737057	0.83[AMR][1000 genomes]
rs73395114	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8033014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036098	0.96[ASN][1000 genomes]
rs8043431	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11858160	SLC24A5	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50424200-50429000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr15:50425200-50429000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:50425800-50428800	Enhancers	Hela-S3	cervix
4	chr15:50425800-50430800	Enhancers	NHDF-Ad	bronchial
5	chr15:50426000-50428800	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:50426000-50429000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:50426000-50429400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:50426000-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:50426000-50430800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:50426400-50428600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:50426400-50430400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:50426400-50430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:50426400-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:50426400-50430600	Enhancers	NHLF	lung
15	chr15:50426400-50430800	Enhancers	Osteobl	bone
16	chr15:50426600-50429000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:50426800-50429000	Enhancers	Stomach Smooth Muscle	stomach
18	chr15:50427000-50428800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:50427200-50429800	Weak transcription	HUVEC	blood vessel
20	chr15:50427400-50428600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:50427600-50429200	Enhancers	Fetal Stomach	stomach
22	chr15:50427600-50429400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:50427800-50429400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:50427800-50429800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:50427800-50429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:50427800-50429800	Weak transcription	HSMM	muscle
27	chr15:50427800-50429800	Weak transcription	NH-A	brain
28	chr15:50427800-50436400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:50428000-50429000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:50428000-50429200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:50428000-50429200	Weak transcription	HMEC	breast
32	chr15:50428000-50429200	Weak transcription	K562	blood
33	chr15:50428000-50429200	Weak transcription	NHEK	skin
34	chr15:50428200-50428800	Enhancers	A549	lung
35	chr15:50428400-50428800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:50428400-50429400	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:50428400-50430400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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