Variant report

Variant	rs478839
Chromosome Location	chr10:89731870-89731871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89724975..89728613-chr10:89729224..89733070,3	K562	blood:
2	chr10:89623124..89624874-chr10:89731308..89733692,2	MCF-7	breast:
3	chr10:89729355..89732120-chr10:89734867..89736636,2	K562	blood:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12255199	0.86[YRI][hapmap]
rs1234214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs559270	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs701848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs806685	0.82[EUR][1000 genomes];0.90[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	esv1793518	chr10:89625582-89733420	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1798260	chr10:89625582-89733420	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv551837	chr10:89707265-89777788	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs478839	SNCG	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89696600-89734600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:89708800-89734400	Weak transcription	Aorta	Aorta
3	chr10:89713000-89733200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:89714600-89738600	Weak transcription	NHEK	skin
5	chr10:89721800-89735800	Weak transcription	A549	lung
6	chr10:89722000-89736000	Weak transcription	NHLF	lung
7	chr10:89724000-89733200	Weak transcription	HSMM	muscle
8	chr10:89724000-89739000	Weak transcription	Adipose Nuclei	Adipose
9	chr10:89724200-89738600	Weak transcription	HMEC	breast
10	chr10:89724200-89738800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:89724400-89733400	Weak transcription	Hela-S3	cervix
12	chr10:89724400-89738200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:89724400-89738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:89724600-89732400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:89724600-89732400	Weak transcription	Ovary	ovary
16	chr10:89724800-89732400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:89724800-89732400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr10:89724800-89734600	Weak transcription	NH-A	brain
19	chr10:89724800-89734800	Weak transcription	Primary B cells from cord blood	blood
20	chr10:89724800-89736200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:89724800-89738400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:89724800-89739400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:89725000-89732600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:89725000-89734600	Weak transcription	GM12878-XiMat	blood
25	chr10:89725800-89735600	Weak transcription	Liver	Liver
26	chr10:89726000-89735600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr10:89726200-89732400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:89726400-89736200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:89726600-89732400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:89726600-89733600	Weak transcription	HUVEC	blood vessel
31	chr10:89726600-89734600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr10:89726600-89739400	Weak transcription	Fetal Thymus	thymus
33	chr10:89727000-89733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:89727800-89734600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr10:89729000-89733000	Weak transcription	Osteobl	bone
36	chr10:89729000-89733600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr10:89729200-89732400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:89729200-89732400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:89729200-89732600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr10:89729200-89733200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr10:89729600-89732400	Weak transcription	NHDF-Ad	bronchial
42	chr10:89729600-89733000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr10:89730200-89734200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:89730600-89735000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr10:89731200-89732000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:89731200-89736800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr10:89731400-89732200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:89731800-89732800	Enhancers	H1 Cell Line	embryonic stem cell

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