Variant report

Variant	rs2059248
Chromosome Location	chr16:72322376-72322377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72321878..72323763-chr16:72669997..72671521,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10492819	0.84[EUR][1000 genomes]
rs1437195	0.82[EUR][1000 genomes]
rs16970769	0.94[CEU][hapmap];0.80[MEX][hapmap]
rs4788632	0.80[ASN][1000 genomes]
rs62053965	0.83[EUR][1000 genomes]
rs9940976	1.00[CEU][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv906897	chr16:72283147-72326375	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2059248	ZFHX3	cis	parietal	SCAN
rs2059248	CALB2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72302600-72332000	Weak transcription	Primary B cells from cord blood	blood
2	chr16:72313400-72323000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr16:72315600-72353600	Weak transcription	Dnd41	blood
4	chr16:72316000-72323400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:72316600-72334800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:72317400-72331800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:72318200-72324200	Enhancers	HMEC	breast
8	chr16:72318600-72324800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:72318600-72329200	Weak transcription	HepG2	liver
10	chr16:72318800-72323600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:72319600-72324800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr16:72320000-72322400	Enhancers	NHEK	skin
13	chr16:72320000-72323600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:72320000-72324200	Weak transcription	Osteobl	bone
15	chr16:72320000-72325200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr16:72320200-72324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:72320400-72325000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:72321000-72323800	Weak transcription	HSMM	muscle
19	chr16:72321000-72324000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr16:72321000-72324400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:72321000-72324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:72321600-72324000	Weak transcription	NHDF-Ad	bronchial
23	chr16:72321800-72323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr16:72321800-72323800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr16:72321800-72324000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:72322200-72323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links