Variant report

Variant	rs7079754
Chromosome Location	chr10:89875683-89875684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89874131..89877304-chr10:89878864..89883197,3	MCF-7	breast:
2	chr10:89874980..89876628-chr10:89878193..89879862,2	K562	blood:
3	chr10:89872939..89875785-chr10:89888334..89891618,3	MCF-7	breast:
4	chr10:89620841..89625888-chr10:89873162..89876316,7	MCF-7	breast:
5	chr10:89620141..89628673-chr10:89867993..89880509,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10749564	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11202654	0.83[AMR][1000 genomes]
rs12416046	0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes]
rs1932532	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4147056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4934378	0.93[ASN][1000 genomes]
rs59204786	0.94[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	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7079754	PCGF5	cis	cerebellum	SCAN
rs7079754	LDB3	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89868200-89876200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:89868400-89876800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:89869600-89881400	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:89872200-89878800	Enhancers	Fetal Thymus	thymus
5	chr10:89872400-89881200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr10:89872600-89877800	Enhancers	Primary hematopoietic stem cells	blood
7	chr10:89872600-89878200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:89872600-89878200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:89872800-89877400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:89872800-89878800	Enhancers	Primary T cells from cord blood	blood
11	chr10:89873200-89876200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:89873200-89878200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:89873800-89876000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr10:89873800-89876200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:89873800-89879000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:89874000-89877800	Weak transcription	Adipose Nuclei	Adipose
17	chr10:89874000-89878000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:89874000-89880200	Weak transcription	Right Atrium	heart
19	chr10:89874000-89881200	Enhancers	Primary B cells from cord blood	blood
20	chr10:89874000-89891400	Weak transcription	Left Ventricle	heart
21	chr10:89874200-89876200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr10:89874200-89876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:89874200-89877800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr10:89874200-89878600	Weak transcription	Stomach Mucosa	stomach
25	chr10:89874400-89876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:89874400-89876200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:89874600-89876000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:89874600-89876000	Enhancers	GM12878-XiMat	blood
29	chr10:89874600-89876200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:89874600-89876600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:89874600-89876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:89874600-89877000	Weak transcription	Spleen	Spleen
33	chr10:89874600-89877200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr10:89874600-89878000	Weak transcription	Liver	Liver
35	chr10:89874600-89878800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr10:89874600-89879800	Weak transcription	Lung	lung
37	chr10:89874600-89880800	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:89874600-89882400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:89874800-89876200	Enhancers	HSMM	muscle
40	chr10:89874800-89877800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr10:89874800-89877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:89875000-89876200	Weak transcription	Dnd41	blood
43	chr10:89875200-89876800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:89875200-89879200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:89875400-89876400	Enhancers	Hela-S3	cervix
46	chr10:89875400-89877200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:89875400-89877200	Enhancers	NH-A	brain
48	chr10:89875400-89877200	Enhancers	NHLF	lung
49	chr10:89875400-89877400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr10:89875400-89877400	Enhancers	HMEC	breast

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