Variant report

Variant	rs2409033
Chromosome Location	chr5:127234574-127234575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:127232675..127235268-chr5:127236126..127238266,2	K562	blood:
2	chr5:127233004..127236913-chr5:127245054..127247507,3	MCF-7	breast:
3	chr5:127232934..127234618-chr5:127322508..127324974,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10042555	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs111941	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs111942	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs122730	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs122731	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs122734	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12332194	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12332385	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332386	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12332552	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421748	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1421749	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1421750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421751	0.85[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151853	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151856	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151858	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151859	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151882	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs1520247	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173444	0.96[ASN][1000 genomes]
rs187381	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193495	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006195	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108653	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245156	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245160	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245172	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245173	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245174	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245175	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245181	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs245186	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs245192	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs245195	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs245221	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245237	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs2544779	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544780	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681512	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2764766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2409033	SLC27A6	cis	parietal	SCAN
rs2409033	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127233600-127234800	Enhancers	Brain Angular Gyrus	brain
2	chr5:127233800-127235200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:127234000-127234800	Enhancers	Brain Hippocampus Middle	brain
4	chr5:127234200-127234800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:127234200-127234800	Enhancers	Brain Anterior Caudate	brain
6	chr5:127234200-127234800	Enhancers	Brain Cingulate Gyrus	brain
7	chr5:127234200-127234800	Enhancers	Brain Substantia Nigra	brain
8	chr5:127234200-127235200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:127234200-127235200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr5:127234200-127235200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:127234200-127235200	Enhancers	HMEC	breast
12	chr5:127234200-127235400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:127234200-127235400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:127234200-127235400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127234200-127235800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:127234400-127234800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:127234400-127235000	Enhancers	A549	lung
18	chr5:127234400-127235000	Enhancers	NHEK	skin
19	chr5:127234400-127235200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:127234400-127235200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:127234400-127235200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:127234400-127235200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:127234400-127235400	Enhancers	NHLF	lung
24	chr5:127234400-127235400	Enhancers	Osteobl	bone

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