Variant report

Variant	rs6874089
Chromosome Location	chr5:58474854-58474855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10036938	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042606	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064744	0.95[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs10077198	0.86[ASN][1000 genomes]
rs10472094	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472095	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077978	0.95[CEU][hapmap];0.86[MEX][hapmap]
rs11948460	0.86[ASN][1000 genomes]
rs12108992	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516263	0.93[ASN][1000 genomes]
rs13357070	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889248	0.90[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs16889254	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16889258	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28540859	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705844	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62357974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450504	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450505	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450508	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450509	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868963	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6869149	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]
rs6883912	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892369	0.93[ASN][1000 genomes]
rs6896497	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7700594	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.93[ASN][1000 genomes]
rs7728221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735375	0.93[ASN][1000 genomes]
rs8180396	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs922436	0.96[ASN][1000 genomes]
rs9292191	0.93[ASN][1000 genomes]
rs9918111	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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
rs6874089	RAB3C	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
3	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
5	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
7	chr5:58464800-58478800	Weak transcription	Hela-S3	cervix
8	chr5:58466200-58479400	Weak transcription	Psoas Muscle	Psoas
9	chr5:58469000-58483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:58469200-58484400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:58469800-58477000	Genic enhancers	A549	lung
12	chr5:58469800-58478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:58470000-58483400	Weak transcription	Fetal Lung	lung
14	chr5:58470200-58481400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:58470600-58480600	Weak transcription	Fetal Heart	heart
16	chr5:58470600-58482000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:58470600-58483800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:58471000-58479000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:58471000-58483600	Weak transcription	Brain Angular Gyrus	brain
20	chr5:58471000-58483800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:58471000-58484800	Weak transcription	Pancreas	Pancrea
22	chr5:58471600-58484200	Weak transcription	Brain Germinal Matrix	brain
23	chr5:58472000-58479000	Weak transcription	Gastric	stomach
24	chr5:58472000-58484400	Weak transcription	Primary B cells from cord blood	blood
25	chr5:58472200-58475200	Weak transcription	Colonic Mucosa	Colon
26	chr5:58472200-58485800	Weak transcription	Stomach Mucosa	stomach
27	chr5:58472400-58480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:58472600-58475800	Weak transcription	Lung	lung
29	chr5:58472600-58476400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:58472800-58475200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:58472800-58475800	Strong transcription	Fetal Intestine Large	intestine
32	chr5:58472800-58476200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:58472800-58484200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:58473000-58475000	Strong transcription	Right Ventricle	heart
35	chr5:58473400-58475200	Strong transcription	Fetal Stomach	stomach
36	chr5:58473400-58476400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr5:58473800-58475000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:58473800-58478600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:58474200-58475000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:58474400-58475000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:58474600-58476600	Enhancers	GM12878-XiMat	blood
43	chr5:58474600-58476800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:58474600-58478600	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:58474600-58478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:58474600-58478800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:58474600-58481200	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:58474600-58483600	Weak transcription	Fetal Brain Female	brain
49	chr5:58474600-58484400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:58474800-58478400	Weak transcription	HSMMtube	muscle

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