Variant report

Variant	rs17796040
Chromosome Location	chr5:58754510-58754511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

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	0.89[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs16889865	0.81[TSI][hapmap]
rs16889869	0.81[TSI][hapmap]
rs16889878	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16889892	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17728654	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795692	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	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17796824	1.00[JPT][hapmap]
rs17797601	1.00[JPT][hapmap]
rs1824154	0.89[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1902610	0.92[EUR][1000 genomes]
rs2081092	0.80[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2081093	1.00[JPT][hapmap]
rs2098699	1.00[JPT][hapmap]
rs4326095	1.00[JPT][hapmap]
rs4551023	1.00[JPT][hapmap]
rs4604141	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173502	1.00[ASN][1000 genomes]
rs56349317	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6450519	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6861969	1.00[JPT][hapmap]
rs6871710	0.86[GIH][hapmap]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7737908	1.00[JPT][hapmap];0.80[AFR][1000 genomes]
rs7738023	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv275451	chr5:58754377-58755220	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17796040	CNTN6	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
2	chr5:58716000-58756600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:58731800-58764800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58735800-58756400	Weak transcription	Psoas Muscle	Psoas
5	chr5:58750400-58756200	Weak transcription	Fetal Stomach	stomach
6	chr5:58750600-58754800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:58751600-58755400	Weak transcription	Fetal Kidney	kidney
8	chr5:58752200-58756600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:58752400-58756400	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:58752600-58754600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58753400-58754600	Enhancers	Liver	Liver
12	chr5:58753400-58754600	Enhancers	Fetal Brain Male	brain
13	chr5:58753400-58755000	Strong transcription	A549	lung
14	chr5:58753600-58767400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:58753800-58755400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr5:58753800-58755800	Enhancers	Fetal Intestine Large	intestine
17	chr5:58753800-58757600	Enhancers	Fetal Intestine Small	intestine
18	chr5:58754200-58754600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:58754200-58754800	Enhancers	Fetal Brain Female	brain
20	chr5:58754400-58754600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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