Variant report

Variant	rs12655922
Chromosome Location	chr5:166999625-166999626
allele	A/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	CTCF	chr5:166999580-166999730	HPF	lung:	n/a	n/a
2	CTCF	chr5:166999620-166999770	HRE	kidney:	n/a	n/a
3	CTCF	chr5:166999580-166999730	AG10803	skin:	n/a	n/a
4	CTCF	chr5:166999600-166999750	AG10803	skin:	n/a	n/a

Variant related genes	Relation type
TENM2	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17068781	1.00[CHB][hapmap];0.94[YRI][hapmap];0.96[ASN][1000 genomes]
rs17068792	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[YRI][hapmap];0.92[ASN][1000 genomes]
rs17068796	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs17068862	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278011	0.96[ASN][1000 genomes]
rs278015	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs59355279	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59726875	0.90[ASN][1000 genomes]
rs60290329	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61216313	0.90[ASN][1000 genomes]
rs6859433	0.90[ASN][1000 genomes]
rs6896383	0.84[AMR][1000 genomes]
rs73380907	0.91[AMR][1000 genomes]
rs73380909	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73380910	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73380913	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73380917	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73381002	0.92[ASN][1000 genomes]
rs73803911	0.90[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	nsv932627	chr5:166744408-167290959	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv883104	chr5:166971457-167037934	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:166996200-167000000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr5:166996800-166999800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:166997000-166999800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:166997000-167000200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:166997000-167000200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:166997000-167000200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:166997000-167000200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:166997000-167000400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:166997200-166999800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:166997200-167000000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:166997200-167000000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:166997200-167000200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:166997200-167000800	Weak transcription	Aorta	Aorta
14	chr5:166997400-167000200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr5:166997400-167000200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:166997600-166999800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:166998000-167000200	Weak transcription	HSMMtube	muscle
18	chr5:166998000-167000400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:166998400-167000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:166999000-167000200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:166999000-167000200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:166999000-167000400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:166999200-167000400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:166999600-167000000	Active TSS	Fetal Brain Male	brain
25	chr5:166999600-167000200	Enhancers	HSMM	muscle
26	chr5:166999600-167000400	Bivalent/Poised TSS	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links