Variant report

Variant	rs6869149
Chromosome Location	chr5:58436920-58436921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10036938	0.93[ASN][1000 genomes]
rs10042606	0.93[ASN][1000 genomes]
rs10064744	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10070295	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10077198	0.93[ASN][1000 genomes]
rs10472094	0.93[ASN][1000 genomes]
rs10472095	0.93[ASN][1000 genomes]
rs1077978	0.91[CEU][hapmap]
rs12108992	0.93[ASN][1000 genomes]
rs12516263	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357070	0.93[ASN][1000 genomes]
rs16889248	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16889254	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540859	0.93[ASN][1000 genomes]
rs28705844	0.89[ASN][1000 genomes]
rs62356728	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62357974	0.93[ASN][1000 genomes]
rs6450504	0.93[ASN][1000 genomes]
rs6450505	0.83[CEU][hapmap];0.93[ASN][1000 genomes]
rs6450508	0.93[ASN][1000 genomes]
rs6450509	0.93[ASN][1000 genomes]
rs6868963	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874089	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[ASN][1000 genomes]
rs6881137	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6883912	0.93[ASN][1000 genomes]
rs6886854	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6892369	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896497	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs736736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7700594	0.93[ASN][1000 genomes]
rs7714707	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716261	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7728221	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs7735375	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180396	0.91[CEU][hapmap]
rs922436	0.89[ASN][1000 genomes]
rs9292191	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918111	0.93[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6869149	RAB3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
2	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
4	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
7	chr5:58430000-58437000	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:58430000-58442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:58431000-58440000	Weak transcription	Fetal Lung	lung
10	chr5:58431200-58437400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58433000-58451600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:58434800-58437800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:58435000-58439600	Genic enhancers	A549	lung
14	chr5:58435200-58438000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr5:58435200-58439000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:58435400-58437200	Weak transcription	Psoas Muscle	Psoas
17	chr5:58435400-58442400	Weak transcription	Hela-S3	cervix
18	chr5:58435800-58437600	Enhancers	Fetal Heart	heart
19	chr5:58436000-58439200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:58436600-58437400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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