Variant report

Variant	rs2505734
Chromosome Location	chr10:44793299-44793300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr10:44793209-44793409	H1-hESC	embryonic stem cell:	n/a	n/a
2	BACH1	chr10:44793208-44793477	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:44790196..44793217-chr10:44793221..44795884,3	MCF-7	breast:
2	chr10:44790481..44792534-chr10:44792786..44795587,2	MCF-7	breast:
3	chr10:44776762..44778812-chr10:44792922..44795604,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229116	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1089042	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1746046	0.85[EUR][1000 genomes]
rs2437934	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2437935	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2476352	0.80[EUR][1000 genomes]
rs475926	0.84[EUR][1000 genomes]
rs605956	0.84[EUR][1000 genomes]
rs754713	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs800317	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs809602	0.84[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv508579	chr10:44709770-44799256	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2505734	ZNF239	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44789200-44796600	Weak transcription	Fetal Brain Female	brain
2	chr10:44790600-44796600	Weak transcription	Aorta	Aorta
3	chr10:44791000-44795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:44791200-44794400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr10:44791200-44795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:44791200-44795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:44791200-44796000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:44791200-44796000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:44791200-44796600	Weak transcription	Left Ventricle	heart
10	chr10:44791200-44796800	Weak transcription	Gastric	stomach
11	chr10:44791200-44805400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:44791400-44794600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:44791400-44795600	Weak transcription	NHLF	lung
14	chr10:44791400-44795800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:44791400-44796000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:44791400-44796000	Weak transcription	GM12878-XiMat	blood
17	chr10:44791400-44796200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:44791400-44796200	Weak transcription	Brain Anterior Caudate	brain
19	chr10:44791400-44796200	Weak transcription	Brain Substantia Nigra	brain
20	chr10:44791400-44796400	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:44791600-44793800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:44791600-44794200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:44791600-44795200	Weak transcription	Brain Germinal Matrix	brain
24	chr10:44791600-44795400	Weak transcription	NHDF-Ad	bronchial
25	chr10:44791600-44795600	Weak transcription	Osteobl	bone
26	chr10:44791600-44796000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:44791600-44796000	Weak transcription	NH-A	brain
28	chr10:44791600-44796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:44791600-44796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:44791600-44796800	Weak transcription	Right Ventricle	heart
31	chr10:44792200-44796600	Weak transcription	Brain Angular Gyrus	brain
32	chr10:44792400-44794400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr10:44792400-44796000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:44792600-44793800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr10:44792800-44794400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr10:44793000-44793400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr10:44793000-44793600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr10:44793200-44793400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:44793200-44793400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:44793200-44793600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr10:44793200-44793600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr10:44793200-44793600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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