Variant report

Variant	rs17795692
Chromosome Location	chr5:58728915-58728916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10514860	1.00[JPT][hapmap]
rs11949561	1.00[JPT][hapmap]
rs12187079	1.00[JPT][hapmap]
rs12187448	1.00[JPT][hapmap]
rs16877169	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16889611	0.87[YRI][hapmap]
rs16889853	0.82[TSI][hapmap]
rs16889878	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs17728654	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740749	1.00[JPT][hapmap]
rs17741233	1.00[JPT][hapmap]
rs17795596	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796040	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796399	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17796824	1.00[JPT][hapmap]
rs17797601	1.00[JPT][hapmap]
rs1824154	0.86[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1902610	0.83[EUR][1000 genomes]
rs2081092	0.90[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2081093	1.00[JPT][hapmap]
rs2098699	1.00[JPT][hapmap]
rs41447947	0.82[TSI][hapmap]
rs4326095	1.00[JPT][hapmap]
rs4551023	1.00[JPT][hapmap]
rs4604141	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173502	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56349317	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6450519	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6861969	1.00[JPT][hapmap]
rs6871710	0.86[GIH][hapmap];0.82[TSI][hapmap]
rs6884572	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7737908	1.00[JPT][hapmap]
rs7738023	0.85[EUR][1000 genomes]

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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17795692	CNTN6	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
3	chr5:58714800-58731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:58716000-58756600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58719400-58738400	Weak transcription	Fetal Intestine Small	intestine
6	chr5:58720000-58730200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:58726200-58731000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:58726600-58730200	Weak transcription	Psoas Muscle	Psoas
9	chr5:58726800-58730400	Weak transcription	Fetal Brain Male	brain
10	chr5:58726800-58731800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:58727000-58731600	Weak transcription	Fetal Brain Female	brain
12	chr5:58727800-58729600	Enhancers	Brain Germinal Matrix	brain
13	chr5:58728000-58729400	Enhancers	Liver	Liver
14	chr5:58728000-58735200	Strong transcription	A549	lung

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