Variant report

Variant	rs11656970
Chromosome Location	chr17:16777177-16777178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10852837	0.97[ASN][1000 genomes]
rs12936318	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2017878	1.00[ASN][1000 genomes]
rs34491921	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35044668	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35113341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4494588	0.94[ASN][1000 genomes]
rs6416869	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6502530	0.94[ASN][1000 genomes]
rs6502533	0.84[ASN][1000 genomes]
rs7208027	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208073	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226311	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279240	0.84[AFR][1000 genomes]
rs8066327	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069906	0.84[ASN][1000 genomes]
rs8081650	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884849	1.00[ASN][1000 genomes]
rs9900143	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905272	1.00[ASN][1000 genomes]
rs9905712	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908336	1.00[ASN][1000 genomes]
rs9908521	1.00[ASN][1000 genomes]
rs9908870	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv907723	chr17:16643881-16777177	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv9498	chr17:16716331-16777806	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv1844622	chr17:16717002-16779412	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv1847753	chr17:16717002-16779412	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv960065	chr17:16758719-16789003	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11656970	LRRC48	cis	parietal	SCAN
rs11656970	COPS3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16775400-16777600	Enhancers	Fetal Intestine Small	intestine
2	chr17:16775600-16777800	Enhancers	Fetal Intestine Large	intestine
3	chr17:16775800-16777400	Enhancers	Liver	Liver
4	chr17:16775800-16777800	Enhancers	Duodenum Mucosa	Duodenum
5	chr17:16776400-16777200	Enhancers	Colonic Mucosa	Colon
6	chr17:16776600-16777200	Enhancers	Fetal Brain Male	brain
7	chr17:16776600-16777200	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr17:16776600-16777200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr17:16776800-16777200	Enhancers	Lung	lung
10	chr17:16776800-16777200	Enhancers	Pancreas	Pancrea
11	chr17:16776800-16777200	Enhancers	Small Intestine	intestine
12	chr17:16776800-16777400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:16776800-16777400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr17:16776800-16777400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr17:16777000-16777200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:16777000-16777200	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr17:16777000-16779200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links