Variant report

Variant	rs11653586
Chromosome Location	chr17:20810647-20810648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10445414	1.00[CEU][hapmap]
rs11204323	0.80[CEU][hapmap]
rs12450680	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279263	0.81[AMR][1000 genomes]
rs4280307	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4452013	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587100	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66762238	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7224181	0.83[MEX][hapmap]
rs7501645	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7501651	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067432	0.82[CHD][hapmap]
rs8067705	1.00[CEU][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8075403	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8075712	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9709208	0.81[ASN][1000 genomes]
rs9897888	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9902946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912643	1.00[CEU][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv978391	chr17:20810355-20811211	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11653586	CCDC144NL,RNASEH1	cis	brain	BrainEAC

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20798200-20811600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:20800200-20811000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:20801800-20812200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:20803200-20811400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:20803400-20811200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:20803400-20811400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr17:20804200-20811800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:20806200-20811000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:20806200-20811400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:20807200-20811400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:20810000-20812800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:20810200-20812600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:20810400-20811200	Enhancers	K562	blood
14	chr17:20810600-20810800	Enhancers	Hela-S3	cervix

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links