Variant report

Variant	rs6515304
Chromosome Location	chr20:23118199-23118200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23117394-23118385	K562	blood:	n/a	n/a
2	POLR2A	chr20:23117431-23118519	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr20:23117427-23118504	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr20:23116862-23118357	K562	blood:	n/a	n/a
5	ZMIZ1	chr20:23117323-23118266	K562	blood:	n/a	n/a
6	POLR2A	chr20:23117390-23118922	K562	blood:	n/a	n/a
7	POLR2A	chr20:23116646-23118432	K562	blood:	n/a	n/a
8	POLR2A	chr20:23116823-23118717	K562	blood:	n/a	n/a
9	CHD2	chr20:23117398-23118286	K562	blood:	n/a	n/a
10	JUN	chr20:23117243-23118831	K562	blood:	n/a	chr20:23117653-23117665 chr20:23117655-23117663

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23039939..23042121-chr20:23116423..23118513,2	K562	blood:
2	chr20:22392151..22394813-chr20:23116563..23119413,2	K562	blood:
3	chr20:23030023..23032778-chr20:23118158..23119760,2	K562	blood:
4	chr20:22892076..22895056-chr20:23117704..23119420,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSTR4-12	chr20:23116598-23118942	ucscGeneNc_uc002wsw_1

No data

Variant related genes	Relation type
LINC00656	TF binding region
ENSG00000178726	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11087414	0.91[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11697283	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12710326	0.84[ASN][1000 genomes]
rs1884658	0.92[ASN][1000 genomes]
rs4813480	0.91[ASN][1000 genomes]
rs4815176	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs55727610	0.83[ASN][1000 genomes]
rs6048561	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6083011	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs6083014	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs6083015	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs6083016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083017	0.83[ASN][1000 genomes]
rs6113954	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs6113957	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6113960	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6515302	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7269464	0.95[ASN][1000 genomes]
rs755697	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs8122415	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs844904	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[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	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6515304	CST3	cis	lymphoblastoid	seeQTL
rs6515304	CST9	cis	cerebellum	SCAN
rs6515304	RIN2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23109000-23120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:23110400-23121600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr20:23111000-23120400	Weak transcription	Pancreas	Pancrea
4	chr20:23112600-23120600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:23114200-23120200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:23114200-23121800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr20:23114600-23119200	Weak transcription	Spleen	Spleen
8	chr20:23114600-23120400	Weak transcription	Fetal Lung	lung
9	chr20:23114600-23121800	Weak transcription	Right Ventricle	heart
10	chr20:23114600-23122800	Weak transcription	Right Atrium	heart
11	chr20:23115800-23122600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr20:23116200-23118400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr20:23116200-23119600	Enhancers	Dnd41	blood
14	chr20:23116400-23119600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr20:23116400-23120000	Enhancers	Esophagus	oesophagus
16	chr20:23116400-23120600	Enhancers	Psoas Muscle	Psoas
17	chr20:23116600-23118400	Enhancers	Fetal Muscle Trunk	muscle
18	chr20:23116600-23119200	Enhancers	Fetal Muscle Leg	muscle
19	chr20:23116800-23118800	Enhancers	Placenta	Placenta
20	chr20:23116800-23118800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr20:23116800-23119000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:23116800-23119400	Enhancers	HSMM	muscle
23	chr20:23116800-23120600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:23116800-23120600	Enhancers	NHEK	skin
25	chr20:23117000-23118200	Enhancers	Hela-S3	cervix
26	chr20:23117000-23119000	Weak transcription	Fetal Thymus	thymus
27	chr20:23117000-23120000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:23117000-23121600	Weak transcription	Adipose Nuclei	Adipose
29	chr20:23117000-23121800	Weak transcription	NHDF-Ad	bronchial
30	chr20:23117200-23120200	Weak transcription	HUVEC	blood vessel
31	chr20:23117600-23118200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr20:23117600-23118200	Enhancers	Left Ventricle	heart
33	chr20:23117600-23118200	Enhancers	Lung	lung
34	chr20:23117600-23118400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:23117800-23118200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr20:23117800-23118200	Flanking Active TSS	K562	blood
37	chr20:23117800-23122200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr20:23117800-23122800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:23118000-23118400	Enhancers	HSMMtube	muscle
40	chr20:23118000-23119600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:23118000-23122000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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