Variant report

Variant	rs5998614
Chromosome Location	chr22:33149936-33149937
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33139149..33141929-chr22:33149411..33151571,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10483165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1074421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11703138	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs11704261	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12157546	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12157560	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484506	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484982	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989438	0.82[ASN][1000 genomes]
rs2013544	0.82[ASN][1000 genomes]
rs57852281	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58237391	0.82[ASN][1000 genomes]
rs5994620	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994622	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998620	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998623	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998624	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998626	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998627	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5998629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518798	0.82[ASN][1000 genomes]
rs7284103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7286761	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7287602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7287772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7289956	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7290713	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7291454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156468	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156471	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156473	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156475	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156480	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156483	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156486	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156494	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73158303	0.82[ASN][1000 genomes]
rs738990	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs762886	0.82[JPT][hapmap]
rs8135298	0.86[YRI][hapmap]
rs8136169	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8139641	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8142064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8142758	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9621568	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5998614	GAL3ST1	cis	parietal	SCAN
rs5998614	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33141600-33150600	Weak transcription	Spleen	Spleen
2	chr22:33142600-33150600	Weak transcription	HMEC	breast
3	chr22:33143000-33150400	Weak transcription	Lung	lung
4	chr22:33143000-33150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr22:33143200-33150600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:33144000-33150400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:33144000-33150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:33144800-33150400	Weak transcription	Left Ventricle	heart
9	chr22:33145800-33150400	Enhancers	HepG2	liver
10	chr22:33147800-33150400	Weak transcription	Liver	Liver
11	chr22:33147800-33150400	Weak transcription	Hela-S3	cervix
12	chr22:33148000-33151200	Enhancers	HSMM	muscle
13	chr22:33148000-33151200	Enhancers	NH-A	brain
14	chr22:33148000-33151200	Enhancers	Osteobl	bone
15	chr22:33148000-33151400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:33148200-33150000	Enhancers	Fetal Stomach	stomach
17	chr22:33148400-33151000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:33148400-33151200	Enhancers	Fetal Muscle Trunk	muscle
19	chr22:33148600-33150000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:33148600-33150000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr22:33148600-33151200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:33148600-33151400	Enhancers	Fetal Muscle Leg	muscle
23	chr22:33148600-33151600	Enhancers	Adipose Nuclei	Adipose
24	chr22:33148800-33151200	Enhancers	HSMMtube	muscle
25	chr22:33149000-33151600	Enhancers	Fetal Intestine Small	intestine
26	chr22:33149200-33150000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr22:33149200-33151800	Enhancers	Fetal Intestine Large	intestine
28	chr22:33149200-33153400	Weak transcription	Fetal Thymus	thymus
29	chr22:33149200-33157200	Weak transcription	NHLF	lung
30	chr22:33149400-33150400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr22:33149400-33152600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr22:33149400-33156600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:33149400-33157400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:33149600-33150600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr22:33149600-33150600	Weak transcription	Right Atrium	heart
36	chr22:33149600-33156400	Weak transcription	Placenta	Placenta
37	chr22:33149600-33157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr22:33149800-33150200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:33149800-33150200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr22:33149800-33150200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:33149800-33150200	Weak transcription	NHDF-Ad	bronchial
42	chr22:33149800-33150400	Weak transcription	Right Ventricle	heart
43	chr22:33149800-33150600	Enhancers	Duodenum Mucosa	Duodenum
44	chr22:33149800-33150800	Enhancers	Duodenum Smooth Muscle	Duodenum

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