Variant report

Variant	rs6475081
Chromosome Location	chr9:16784127-16784128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10733321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10810618	1.00[JPT][hapmap]
rs10810623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289196	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330300	1.00[JPT][hapmap]
rs1330301	0.87[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026803	1.00[ASN][1000 genomes]
rs2243614	1.00[JPT][hapmap]
rs2243836	1.00[ASN][1000 genomes]
rs2254193	1.00[JPT][hapmap]
rs2254468	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2480924	1.00[ASN][1000 genomes]
rs3927535	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961756	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961759	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475071	1.00[JPT][hapmap]
rs6475079	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037653	1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850168	0.87[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859111	0.87[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7860932	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7873181	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407777	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475081	CNTN6	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16754000-16787000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:16762600-16786800	Weak transcription	NHLF	lung
3	chr9:16767600-16795400	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:16768000-16795000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:16769400-16784800	Weak transcription	Fetal Intestine Large	intestine
6	chr9:16769800-16787600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:16769800-16795400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:16770000-16786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:16772400-16784400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:16773000-16795000	Weak transcription	HSMMtube	muscle
11	chr9:16773800-16785000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:16774000-16784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:16774200-16787400	Weak transcription	NH-A	brain
14	chr9:16775600-16784400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:16775800-16784600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:16776000-16786600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16776000-16787600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:16776200-16784400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:16776200-16787400	Weak transcription	Osteobl	bone
20	chr9:16778400-16787400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:16778800-16787200	Weak transcription	NHDF-Ad	bronchial
22	chr9:16779000-16787200	Weak transcription	Psoas Muscle	Psoas
23	chr9:16781600-16784400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:16782600-16785400	Enhancers	Colon Smooth Muscle	Colon
25	chr9:16782800-16787400	Weak transcription	HUVEC	blood vessel
26	chr9:16783000-16786800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:16783400-16785200	Weak transcription	Fetal Stomach	stomach
28	chr9:16783400-16787400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:16783600-16784200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:16783600-16784800	Weak transcription	Fetal Kidney	kidney
31	chr9:16784000-16784600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr9:16784000-16784600	Enhancers	HSMM	muscle
33	chr9:16784000-16785200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr9:16784000-16786000	Enhancers	Ovary	ovary

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