Variant report

Variant	rs2299138
Chromosome Location	chr7:39391875-39391876
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10255235	0.85[ASN][1000 genomes]
rs10256992	0.90[CHD][hapmap]
rs10258232	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10265404	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10282049	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11514785	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11981229	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12666115	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12672997	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13438025	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17701573	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2073538	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2074936	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237413	0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2237414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299136	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800853	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55751785	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58695218	0.89[ASN][1000 genomes]
rs6462913	0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6462914	0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6979897	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7801145	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7807957	0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][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	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39389600-39392400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:39389600-39392600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:39389600-39392800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:39389600-39392800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:39389600-39393200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr7:39389600-39393600	Weak transcription	Brain Angular Gyrus	brain
7	chr7:39389600-39395000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:39389600-39395000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:39389800-39393600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:39390200-39393400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr7:39390400-39395000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:39391000-39393400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:39391200-39393200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:39391200-39393400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:39391400-39393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:39391400-39394600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:39391400-39394800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr7:39391800-39392400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:39391800-39392600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:39391800-39393200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:39391800-39394400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links