Variant report

Variant	rs277984
Chromosome Location	chr5:70930966-70930967
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70929199..70932384-chr5:70932859..70936890,5	MCF-7	breast:
2	chr5:70883251..70886427-chr5:70928765..70931034,4	MCF-7	breast:
3	chr5:70930390..70934601-chr5:70935196..70939070,4	K562	blood:
4	chr5:70865719..70868143-chr5:70930530..70933476,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs157192	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs157193	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs169406	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs182191	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277927	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277941	0.82[AMR][1000 genomes]
rs277951	0.89[ASN][1000 genomes]
rs277952	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs277953	0.90[ASN][1000 genomes]
rs277955	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277956	0.88[ASN][1000 genomes]
rs277975	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs277977	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs277982	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277983	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277987	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277988	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277989	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277990	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277991	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277992	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277993	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277994	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs277998	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs282357	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs368462	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs388918	0.82[AMR][1000 genomes]
rs411050	0.80[AMR][1000 genomes]
rs412766	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs457539	0.85[ASN][1000 genomes]
rs457889	0.82[AMR][1000 genomes]
rs458829	0.82[AMR][1000 genomes]
rs461690	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs461942	0.82[AMR][1000 genomes]
rs462534	0.82[AMR][1000 genomes]
rs464639	0.82[AMR][1000 genomes]
rs467880	0.82[AMR][1000 genomes]
rs467883	0.82[AMR][1000 genomes]
rs468010	0.82[AMR][1000 genomes]
rs468796	0.82[AMR][1000 genomes]
rs4703617	0.89[ASN][1000 genomes]
rs617876	0.82[AMR][1000 genomes]

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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv933076	chr5:70927790-70931298	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933359	chr5:70927969-70931298	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv328811	chr5:70928971-70936086	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs277984	MRPS27	cis	cerebellum	SCAN
rs277984	GFM2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
2	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
3	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
5	chr5:70898200-70944200	Weak transcription	Osteobl	bone
6	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
7	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
9	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:70900400-70931000	Weak transcription	K562	blood
12	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
14	chr5:70907400-70932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:70909200-70931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:70912200-70931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:70912400-70936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:70912600-70943800	Weak transcription	A549	lung
21	chr5:70913000-70934200	Weak transcription	Fetal Brain Female	brain
22	chr5:70914200-70938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:70915400-70950800	Weak transcription	NHLF	lung
25	chr5:70917000-70936400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:70917000-70945000	Weak transcription	Hela-S3	cervix
27	chr5:70917200-70937800	Weak transcription	Aorta	Aorta
28	chr5:70917200-70942000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:70917400-70942600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:70918000-70942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:70919400-70934800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:70919800-70955000	Weak transcription	HUVEC	blood vessel
33	chr5:70920200-70932200	Weak transcription	Fetal Intestine Small	intestine
34	chr5:70923200-70936400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:70923200-70937600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:70925400-70950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:70926400-70932200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr5:70926600-70933600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:70926600-70954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:70926800-70931600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:70926800-70931600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:70926800-70931600	Strong transcription	GM12878-XiMat	blood
43	chr5:70927000-70931600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr5:70927000-70931600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:70927000-70931600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:70927000-70933000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:70927000-70939600	Strong transcription	Fetal Intestine Large	intestine
48	chr5:70927000-70939800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:70927000-70954000	Strong transcription	Dnd41	blood
50	chr5:70927000-70954200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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