Variant report

Variant	rs7728221
Chromosome Location	chr5:58465539-58465540
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10036938	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10042606	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10064744	0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs10077198	0.83[ASN][1000 genomes]
rs10472094	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10472095	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077978	0.95[CEU][hapmap];0.81[MEX][hapmap]
rs11948460	0.82[ASN][1000 genomes]
rs12108992	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12516263	0.89[ASN][1000 genomes]
rs13357070	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889248	0.90[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs16889254	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs16889258	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs28540859	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28705844	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62356728	0.80[EUR][1000 genomes]
rs62357974	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450504	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450505	0.89[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450508	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450509	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868963	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6869149	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]
rs6874089	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]
rs6883912	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6892369	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6896497	0.94[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736736	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7700594	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7714707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.89[ASN][1000 genomes]
rs7735375	0.89[ASN][1000 genomes]
rs8180396	0.95[CEU][hapmap]
rs922436	0.93[ASN][1000 genomes]
rs9292191	0.89[ASN][1000 genomes]
rs9918111	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs7728221	RAB3C	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58447600-58473200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58447600-58473400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
5	chr5:58449400-58473600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:58454400-58472800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:58455200-58473400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58455800-58473600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:58457800-58473400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:58459400-58473400	Weak transcription	Fetal Stomach	stomach
12	chr5:58460000-58472600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:58460800-58469400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
15	chr5:58461600-58467000	Genic enhancers	A549	lung
16	chr5:58463800-58466200	Enhancers	Colon Smooth Muscle	Colon
17	chr5:58464000-58465600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
19	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
20	chr5:58464400-58465600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:58464400-58465800	Enhancers	HSMM	muscle
22	chr5:58464400-58465800	Enhancers	HSMMtube	muscle
23	chr5:58464400-58473000	Weak transcription	Right Ventricle	heart
24	chr5:58464600-58474400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:58464800-58478800	Weak transcription	Hela-S3	cervix
26	chr5:58465000-58466000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:58465200-58465600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:58465400-58465600	Enhancers	Rectal Smooth Muscle	rectum
29	chr5:58465400-58465600	Enhancers	Right Atrium	heart
30	chr5:58465400-58465800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:58465400-58466000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:58465400-58466200	Enhancers	Psoas Muscle	Psoas

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