Variant report

Variant	rs2804925
Chromosome Location	chr6:13574935-13574936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:46)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:46 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
2	chr6:13574638..13575386-chr7:117823501..117824120,2	Hela-S3	cervix:
3	chr6:13572897..13576165-chr6:13619318..13622919,5	K562	blood:
4	chr6:13573088..13576408-chr6:13709684..13713261,5	MCF-7	breast:
5	chr15:93352658..93353196-chr6:13574785..13575714,3	Hela-S3	cervix:
6	chr6:13572710..13576955-chr6:13610549..13618685,22	MCF-7	breast:
7	chr6:13326831..13329117-chr6:13574155..13576632,2	K562	blood:
8	chr6:13484642..13487748-chr6:13572714..13576594,3	K562	blood:
9	chr5:151151845..151152390-chr6:13574797..13575459,2	Hela-S3	cervix:
10	chr1:28995095..28995809-chr6:13574451..13575261,2	HCT-116	colon:
11	chr6:13573221..13576787-chr6:13710917..13713733,6	K562	blood:
12	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
13	chr1:11967945..11968545-chr6:13574677..13575291,2	Hela-S3	cervix:
14	chr4:99850217..99850807-chr6:13574209..13575136,2	Hela-S3	cervix:
15	chr6:13535769..13538764-chr6:13574933..13577249,3	MCF-7	breast:
16	chr6:13574818..13575379-chr7:25164041..25164955,2	Hela-S3	cervix:
17	chr6:13574892..13575841-chr6:13614462..13615340,2	K562	blood:
18	chr20:55966356..55966956-chr6:13574476..13575248,2	Hela-S3	cervix:
19	chr16:10837378..10837940-chr6:13574735..13575248,2	Hela-S3	cervix:
20	chr6:13573004..13578027-chr6:13613856..13617870,10	MCF-7	breast:
21	chr6:13572493..13576795-chr6:13677578..13681816,6	K562	blood:
22	chr19:14800503..14801080-chr6:13574758..13575318,2	Hela-S3	cervix:
23	chr6:13406137..13408577-chr6:13573927..13576170,2	MCF-7	breast:
24	chr6:13572923..13577086-chr6:13614342..13617597,6	K562	blood:
25	chr6:13573217..13575552-chr6:13711779..13713289,2	K562	blood:
26	chr6:13574510..13576795-chr6:13678124..13681559,3	K562	blood:
27	chr6:13572531..13574981-chr6:13813241..13815537,2	K562	blood:
28	chr5:114879958..114880695-chr6:13574785..13575475,2	Hela-S3	cervix:
29	chr1:160312894..160313447-chr6:13574629..13575506,2	HCT-116	colon:
30	chr6:13574305..13575294-chr8:103665947..103666716,2	Hela-S3	cervix:
31	chr12:56551727..56552536-chr6:13574659..13575232,2	Hela-S3	cervix:
32	chr19:1875967..1876544-chr6:13574476..13575318,2	Hela-S3	cervix:
33	chr6:13574530..13575381-chr6:33588931..33589769,3	Hela-S3	cervix:
34	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
35	chr6:13572897..13576165-chr6:13620913..13622919,3	K562	blood:
36	chr12:52449698..52450253-chr6:13574721..13575261,2	Hela-S3	cervix:
37	chr4:25161465..25162427-chr6:13574449..13575337,2	Hela-S3	cervix:
38	chr11:93474297..93475105-chr6:13574782..13575543,2	Hela-S3	cervix:
39	chr6:13274197..13275936-chr6:13573987..13576342,2	K562	blood:
40	chr6:13574683..13575262-chr9:139581559..139582101,2	Hela-S3	cervix:
41	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
42	chr6:13572865..13577994-chr6:13612366..13619020,17	K562	blood:
43	chr14:100704311..100704901-chr6:13574734..13575396,2	Hela-S3	cervix:
44	chr6:13280798..13285135-chr6:13573249..13575552,3	K562	blood:
45	chr6:13327393..13331113-chr6:13573725..13577168,7	MCF-7	breast:
46	chr14:67825632..67826631-chr6:13574719..13575473,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000151247	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000261526	Chromatin interaction
ENSG00000160961	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000050393	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000131355	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000132819	Chromatin interaction
ENSG00000172115	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000177556	Chromatin interaction
ENSG00000162736	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000145780	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000258982	Chromatin interaction
ENSG00000122218	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000128534	Chromatin interaction
ENSG00000100811	Chromatin interaction
ENSG00000100554	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000169692	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000103274	Chromatin interaction
ENSG00000162419	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000268059	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000272379	Chromatin interaction
ENSG00000252966	Chromatin interaction
ENSG00000145907	Chromatin interaction
ENSG00000109618	Chromatin interaction
ENSG00000038210	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11753306	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2328676	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2804910	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804911	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804914	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804917	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs2804919	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804920	0.94[ASN][1000 genomes]
rs2804922	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2804924	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2804926	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2804927	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841505	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]
rs2841506	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841507	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841508	0.97[ASN][1000 genomes]
rs2841509	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2841511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4712037	0.84[AMR][1000 genomes];0.97[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	esv3367329	chr6:13573423-13576971	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2804925	SIRT5	cis	cerebellum	SCAN
rs2804925	SIRT5	cis	Thyroid	GTEx
rs2804925	SIRT5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13573400-13575800	Active TSS	A549	lung
2	chr6:13573600-13575600	Active TSS	Right Ventricle	heart
3	chr6:13573800-13575000	Active TSS	Fetal Muscle Trunk	muscle
4	chr6:13573800-13575600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:13573800-13575600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:13573800-13575600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:13573800-13575600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:13573800-13575600	Active TSS	Brain Angular Gyrus	brain
9	chr6:13573800-13575600	Active TSS	Psoas Muscle	Psoas
10	chr6:13573800-13575800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:13573800-13575800	Active TSS	Brain Germinal Matrix	brain
12	chr6:13574000-13575200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:13574000-13575400	Active TSS	Lung	lung
14	chr6:13574000-13575600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:13574000-13575600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:13574000-13575600	Active TSS	Aorta	Aorta
17	chr6:13574000-13575600	Active TSS	Colon Smooth Muscle	Colon
18	chr6:13574000-13575600	Active TSS	Gastric	stomach
19	chr6:13574000-13575600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr6:13574000-13575600	Transcr. at gene 5' and 3'	Right Atrium	heart
21	chr6:13574000-13575600	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr6:13574000-13575600	Active TSS	NHDF-Ad	bronchial
23	chr6:13574000-13575600	Active TSS	NHLF	lung
24	chr6:13574000-13575800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:13574000-13575800	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr6:13574000-13575800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:13574000-13575800	Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:13574000-13575800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:13574000-13575800	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:13574000-13575800	Active TSS	Fetal Brain Female	brain
31	chr6:13574000-13576000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:13574000-13576000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:13574000-13576000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:13574000-13576200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:13574200-13575000	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr6:13574200-13575000	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr6:13574200-13575000	Active TSS	HepG2	liver
38	chr6:13574200-13575000	Active TSS	NH-A	brain
39	chr6:13574200-13575200	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr6:13574200-13575200	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:13574200-13575200	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr6:13574200-13575200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:13574200-13575200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:13574200-13575200	Active TSS	Placenta	Placenta
45	chr6:13574200-13575200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr6:13574200-13575200	Active TSS	HMEC	breast
47	chr6:13574200-13575200	Active TSS	K562	blood
48	chr6:13574200-13575400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:13574200-13575400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr6:13574200-13575400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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