Variant report

Variant	rs2160046
Chromosome Location	chr4:15453870-15453871
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	chr4:15444346..15446758-chr4:15452590..15454838,2	MCF-7	breast:
2	chr4:15451138..15453425-chr4:15453445..15455847,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10002931	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10003338	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10032941	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10212844	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10212901	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10213628	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1024758	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1024759	0.80[EUR][1000 genomes]
rs10461112	0.85[EUR][1000 genomes]
rs1048037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934015	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11937671	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13104095	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs13106702	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120744	0.83[EUR][1000 genomes]
rs13123785	0.81[CEU][hapmap]
rs13124324	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13129124	0.80[EUR][1000 genomes]
rs13131227	0.82[CHD][hapmap]
rs13132604	0.84[CEU][hapmap]
rs16891939	0.80[EUR][1000 genomes]
rs17469724	0.83[EUR][1000 genomes]
rs2160043	0.84[JPT][hapmap]
rs2192363	0.94[ASN][1000 genomes]
rs2192364	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2215810	0.94[ASN][1000 genomes]
rs28376639	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28561808	0.85[EUR][1000 genomes]
rs2872704	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34400909	0.83[EUR][1000 genomes]
rs35539860	0.84[EUR][1000 genomes]
rs3797006	0.82[CEU][hapmap]
rs3822296	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140932	0.94[ASN][1000 genomes]
rs6449138	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68012715	0.84[EUR][1000 genomes]
rs6828721	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855244	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71601477	0.83[EUR][1000 genomes]
rs7661287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681816	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7687272	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7690471	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7697778	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973629	0.94[ASN][1000 genomes]
rs9991652	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160046	SLC39A8	trans	cerebellum	SCAN
rs2160046	HS3ST1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15438400-15458800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:15438800-15471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:15448400-15458800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:15451800-15454800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:15451800-15454800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:15452200-15454200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr4:15452200-15454800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:15452200-15454800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:15452200-15454800	Enhancers	Aorta	Aorta
10	chr4:15452400-15454200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:15452400-15454200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:15452400-15454200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr4:15452400-15454200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:15452400-15454200	Enhancers	Rectal Smooth Muscle	rectum
15	chr4:15452400-15454200	Enhancers	Right Ventricle	heart
16	chr4:15452400-15454200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:15452400-15454400	Enhancers	Colon Smooth Muscle	Colon
18	chr4:15452400-15454400	Enhancers	Placenta	Placenta
19	chr4:15452400-15454400	Enhancers	HSMMtube	muscle
20	chr4:15452400-15454600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:15452400-15454600	Enhancers	Fetal Stomach	stomach
22	chr4:15452400-15454800	Enhancers	HMEC	breast
23	chr4:15452600-15454000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:15452600-15454200	Enhancers	Right Atrium	heart
25	chr4:15452600-15454200	Enhancers	Stomach Mucosa	stomach
26	chr4:15452600-15454400	Enhancers	Hela-S3	cervix
27	chr4:15452600-15454600	Enhancers	Adipose Nuclei	Adipose
28	chr4:15452600-15454800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:15452600-15454800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:15452600-15456600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:15452800-15454400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:15453000-15454000	Enhancers	Fetal Lung	lung
33	chr4:15453000-15454200	Enhancers	Fetal Heart	heart
34	chr4:15453000-15458800	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:15453200-15454000	Flanking Active TSS	A549	lung
36	chr4:15453200-15454000	Flanking Active TSS	NHEK	skin
37	chr4:15453400-15454200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:15453400-15454200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:15453400-15454800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:15453400-15455800	Enhancers	NHLF	lung
41	chr4:15453400-15456600	Weak transcription	Liver	Liver
42	chr4:15453400-15458200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:15453400-15458400	Weak transcription	Primary B cells from cord blood	blood
44	chr4:15453400-15458600	Weak transcription	Left Ventricle	heart
45	chr4:15453600-15454000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr4:15453600-15454800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:15453600-15454800	Enhancers	HSMM	muscle
48	chr4:15453600-15456600	Weak transcription	Ovary	ovary
49	chr4:15453600-15456600	Weak transcription	Psoas Muscle	Psoas
50	chr4:15453600-15456800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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