Variant report

Variant	rs2841505
Chromosome Location	chr6:13571595-13571596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13571489-13572063	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr6:13571500-13571650	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:13571322-13571768	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr6:13571418-13571842	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr6:13571397-13575713	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:13571450-13571727	HCT-116	colon:	n/a	n/a
7	POLR2A	chr6:13571349-13572399	HCT-116	colon:	n/a	n/a
8	POLR2A	chr6:13571411-13571756	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:13571384-13572142	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:13571580-13571711	A549	lung:	n/a	n/a
11	POLR2A	chr6:13571433-13573078	K562	blood:	n/a	n/a
12	POLR2A	chr6:13571465-13571727	A549	lung:	n/a	n/a
13	POLR2A	chr6:13571590-13571734	A549	lung:	n/a	n/a
14	POLR2A	chr6:13571537-13573248	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:13571237-13575938	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr6:13571324-13573431	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:13571452-13571750	ProgFib	skin:	n/a	n/a
18	POLR2A	chr6:13571477-13576346	MCF10A-Er-Src	breast:	n/a	n/a
19	CEBPB	chr6:13571496-13571716	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:13571250-13574366	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr6:13571465-13571680	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:46821773..46824180-chr6:13571587..13574488,2	MCF-7	breast:
2	chr6:13562426..13565050-chr6:13570346..13572936,3	MCF-7	breast:
3	chr6:13396129..13398707-chr6:13570124..13572077,2	MCF-7	breast:
4	chr6:13471106..13473285-chr6:13571485..13573042,2	K562	blood:

No data

Variant related genes	Relation type
SIRT5	TF binding region
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11753306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804910	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804911	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804916	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804917	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804919	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804920	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2804922	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804924	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804925	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804926	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2804927	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2841506	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2841507	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2841508	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2841509	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2841511	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712037	0.97[AMR][1000 genomes];0.98[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2841505	SIRT5	cis	cerebellum	SCAN
rs2841505	SIRT5	cis	multi-tissue	Pritchard
rs2841505	SIRT5	cis	Thyroid	GTEx
rs2841505	SIRT5	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13560400-13573800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13562800-13573600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:13567000-13573000	Weak transcription	K562	blood
4	chr6:13568200-13573400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:13569000-13573400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:13569000-13573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:13570000-13571800	Weak transcription	Liver	Liver
8	chr6:13570200-13573600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:13570200-13573800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:13570400-13573200	Weak transcription	HepG2	liver
11	chr6:13570400-13573800	Weak transcription	Spleen	Spleen
12	chr6:13570600-13573600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:13570600-13573800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:13570800-13573600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:13571000-13572800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:13571000-13573600	Weak transcription	Fetal Stomach	stomach
17	chr6:13571200-13572600	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:13571200-13573600	Weak transcription	HSMM	muscle
19	chr6:13571400-13571800	Enhancers	Primary neutrophils fromperipheralblood	blood

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