Variant report

Variant	rs16878397
Chromosome Location	chr5:60065519-60065520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10062839	0.82[TSI][hapmap]
rs10939874	0.81[CEU][hapmap]
rs12696975	0.97[EUR][1000 genomes]
rs13153359	1.00[CEU][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs13159372	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs13186761	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13358053	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1445292	0.85[TSI][hapmap]
rs158916	0.81[CEU][hapmap]
rs158920	0.81[CEU][hapmap]
rs158928	0.81[CEU][hapmap]
rs1609041	0.81[CEU][hapmap]
rs1824531	0.89[EUR][1000 genomes]
rs2306350	0.81[CEU][hapmap]
rs2306351	0.81[CEU][hapmap]
rs35006499	0.80[EUR][1000 genomes]
rs4647078	0.81[CEU][hapmap]
rs4647108	0.81[CEU][hapmap]
rs4647168	0.81[CEU][hapmap]
rs4700392	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs6449502	0.81[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6449504	0.85[TSI][hapmap]
rs6449505	0.82[TSI][hapmap]
rs6449509	0.81[CEU][hapmap]
rs6449510	0.81[CEU][hapmap]
rs6869332	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs6871557	0.81[CEU][hapmap]
rs6876346	0.81[EUR][1000 genomes]
rs6877849	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs6896680	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap]
rs702564	1.00[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs7712473	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7714071	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16878397	CWC27	cis	parietal	SCAN
rs16878397	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs16878397	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60040800-60066600	Weak transcription	Fetal Intestine Small	intestine
2	chr5:60044800-60081600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:60044800-60098000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:60045200-60084400	Weak transcription	Brain Angular Gyrus	brain
5	chr5:60057600-60092200	Weak transcription	Brain Anterior Caudate	brain
6	chr5:60057600-60093200	Weak transcription	Pancreas	Pancrea
7	chr5:60057800-60074800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:60058000-60066200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:60060600-60069600	Weak transcription	Esophagus	oesophagus
10	chr5:60061600-60066000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:60061800-60067800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:60061800-60075200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:60062800-60067600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:60064200-60065600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:60065000-60065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:60065000-60065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:60065200-60091800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:60065200-60101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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