Variant report

Variant	rs2804924
Chromosome Location	chr6:13574342-13574343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13573481-13575699	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:13574091-13575803	PFSK-1	brain:	n/a	n/a
3	CTCF	chr6:13574300-13574450	HRE	kidney:	n/a	n/a
4	MAX	chr6:13573740-13575770	HepG2	liver:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
5	RAD21	chr6:13574263-13574671	H1-hESC	embryonic stem cell:	n/a	chr6:13574644-13574658 chr6:13574528-13574542
6	HEY1	chr6:13574258-13575725	HepG2	liver:	n/a	chr6:13574956-13574971 chr6:13574517-13574532 chr6:13574462-13574477 chr6:13574706-13574721
7	POLR2A	chr6:13573785-13575707	K562	blood:	n/a	n/a
8	E2F6	chr6:13573834-13575779	H1-hESC	embryonic stem cell:	n/a	chr6:13574810-13574819 chr6:13574693-13574702 chr6:13573938-13573949 chr6:13574489-13574498
9	IRF1	chr6:13574120-13575745	K562	blood:	n/a	chr6:13574809-13574823
10	MAX	chr6:13573847-13574374	H1-hESC	embryonic stem cell:	n/a	chr6:13574087-13574096 chr6:13574086-13574097
11	RCOR1	chr6:13573945-13575808	K562	blood:	n/a	n/a
12	ZBTB33	chr6:13574304-13574918	SK-N-SH	brain:	n/a	chr6:13574620-13574635
13	POLR2A	chr6:13574328-13575721	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr6:13574300-13574654	K562	blood:	n/a	chr6:13574528-13574542
15	CTCF	chr6:13574328-13574624	GM12878	blood:	n/a	chr6:13574453-13574466 chr6:13574526-13574539
16	POLR2A	chr6:13574217-13575721	GM12892	blood:	n/a	n/a
17	RAD21	chr6:13574268-13574787	SK-N-SH_RA	brain:	n/a	chr6:13574644-13574658 chr6:13574528-13574542
18	CTCF	chr6:13574333-13574617	K562	blood:	n/a	chr6:13574453-13574466 chr6:13574526-13574539
19	CBX3	chr6:13573678-13575818	K562	blood:	n/a	n/a
20	POLR2A	chr6:13573659-13575749	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:13574155-13575695	NB4	blood:	n/a	n/a
22	BHLHE40	chr6:13573895-13575697	K562	blood:	n/a	chr6:13574455-13574471 chr6:13574644-13574660
23	BHLHE40	chr6:13573928-13575695	HepG2	liver:	n/a	chr6:13574455-13574471 chr6:13574644-13574660
24	POLR2A	chr6:13574046-13575656	GM18951	blood:	n/a	n/a
25	POLR2A	chr6:13574249-13575711	Raji	blood:	n/a	n/a
26	POLR2A	chr6:13574217-13575636	HCT-116	colon:	n/a	n/a
27	MYC	chr6:13573890-13575711	Hela-S3	cervix:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
28	MAX	chr6:13573962-13575744	Hela-S3	cervix:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
29	MYC	chr6:13573735-13575740	MCF10A-Er-Src	breast:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
30	MYC	chr6:13574050-13575720	K562	blood:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
31	POLR2A	chr6:13573641-13575660	PBDE	blood:	n/a	n/a
32	CTCF	chr6:13574049-13575823	K562	blood:	n/a	chr6:13574453-13574466 chr6:13574526-13574539 chr6:13575618-13575639 chr6:13575625-13575638 chr6:13575623-13575641 chr6:13575629-13575638
33	TBP	chr6:13574032-13575735	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAZ	chr6:13574022-13575758	K562	blood:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
35	MAX	chr6:13573772-13575705	MCF-7	breast:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
36	EGR1	chr6:13574180-13575812	HCT-116	colon:	n/a	chr6:13574809-13574819 chr6:13574640-13574647 chr6:13574667-13574681 chr6:13574693-13574702 chr6:13574810-13574820
37	ZNF143	chr6:13574283-13575796	GM12878	blood:	n/a	chr6:13574802-13574820 chr6:13574764-13574779 chr6:13574326-13574345 chr6:13574550-13574560
38	POLR2A	chr6:13574056-13575611	Gliobla	brain:	n/a	n/a
39	TCF3	chr6:13574303-13575009	GM12878	blood:	n/a	n/a
40	TCF12	chr6:13574331-13575756	A549	lung:	n/a	chr6:13575641-13575648
41	POLR2A	chr6:13573504-13575741	HepG2	liver:	n/a	n/a
42	CHD2	chr6:13573870-13575705	Hela-S3	cervix:	n/a	chr6:13574811-13574821 chr6:13574840-13574850
43	RAD21	chr6:13574006-13574675	IMR90	lung:	n/a	chr6:13574644-13574658 chr6:13574528-13574542
44	MAX	chr6:13573794-13574362	MCF-7	breast:	n/a	chr6:13574087-13574096 chr6:13574086-13574097
45	MYC	chr6:13573778-13575771	K562	blood:	n/a	chr6:13575017-13575027 chr6:13574087-13574096 chr6:13574086-13574097
46	POLR2A	chr6:13573794-13575765	HUVEC	blood vessel:	n/a	n/a
47	FOXM1	chr6:13574328-13574762	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:13574227-13575736	GM12892	blood:	n/a	n/a
49	BRCA1	chr6:13573978-13574847	H1-hESC	embryonic stem cell:	n/a	chr6:13574622-13574631
50	POLR2A	chr6:13574036-13575087	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:13574296-13574346	Jurkat	blood:	n/a
2	chr6:13574296-13574346	HCT-116	colon:	n/a
3	chr6:13574296-13574346	SK-N-SH	brain:	n/a
4	chr6:13574296-13574346	CMK	blood:	n/a
5	chr6:13574296-13574346	T-47D	breast:	n/a
6	chr6:13574296-13574346	AG04450	lung:	fetal
7	chr6:13574296-13574346	HPAEpiC	pulmonary alveolar:	n/a
8	chr6:13574296-13574346	Hepatocyte	liver:	n/a
9	chr6:13574296-13574346	Caco-2	colon:	n/a
10	chr6:13574296-13574346	HRPEpiC	eye:	n/a
11	chr6:13574296-13574346	GM06990	blood:	n/a
12	chr6:13574296-13574346	HUVEC	blood vessel:	n/a
13	chr6:13574296-13574346	NHBE	bronchial:	n/a
14	chr6:13574296-13574346	HCPEpiC	choroid plexus:	n/a
15	chr6:13574296-13574346	BJ	skin:	n/a
16	chr6:13574296-13574346	U87	brain:	n/a
17	chr6:13574296-13574346	MCF10A-Er-Src	breast:	n/a
18	chr6:13574296-13574346	MCF-7	breast:	n/a
19	chr6:13574296-13574346	HCF	heart:	n/a
20	chr6:13574296-13574346	PFSK-1	brain:	n/a
21	chr6:13574296-13574346	HepG2	liver:	n/a
22	chr6:13574296-13574346	PANC-1	pancreas:	n/a
23	chr6:13574296-13574346	SK-N-SH_RA	brain:	n/a
24	chr6:13574296-13574346	HEEpiC	esophagus:	n/a
25	chr6:13574296-13574346	HL-60	blood:	n/a
26	chr6:13574296-13574346	NT2-D1	testis:	n/a
27	chr6:13574296-13574346	IMR90	lung:	fetal
28	chr6:13574296-13574346	HNPCEpiC	eye:	n/a
29	chr6:13574296-13574346	AG09309	skin:	n/a
30	chr6:13574296-13574346	HRE	kidney:	n/a
31	chr6:13574296-13574346	HIPEpiC	eye:	n/a
32	chr6:13574296-13574346	HMEC	breast:	n/a
33	chr6:13574296-13574346	HRCEpiC	kidney:	n/a
34	chr6:13574296-13574346	SAEC	small airway:	n/a
35	chr6:13574296-13574346	LNCaP	prostate:	n/a
36	chr6:13574296-13574346	GM12878	blood:	n/a
37	chr6:13574296-13574346	GM12891	blood:	n/a
38	chr6:13574296-13574346	AG09319	gingival:	n/a
39	chr6:13574296-13574346	PrEC	prostate:	n/a
40	chr6:13574296-13574346	AG10803	skin:	n/a
41	chr6:13574296-13574346	HAEpiC	amniotic membrane:	n/a
42	chr6:13574296-13574346	HCM	heart:	n/a
43	chr6:13574296-13574346	SKMC	muscle:	n/a
44	chr6:13574296-13574346	RPTEC	kidney:	n/a
45	chr6:13574296-13574346	AoSMC	blood vessel:	n/a
46	chr6:13574296-13574346	AG04449	skin:	fetal
47	chr6:13574296-13574346	ProgFib	skin:	n/a
48	chr6:13574296-13574346	HEK293	kidney:	embryo
49	chr6:13574296-13574346	NHDF-neo	bronchial:	n/a
50	chr6:13574296-13574346	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
2	chr6:13572897..13576165-chr6:13619318..13622919,5	K562	blood:
3	chr6:13573088..13576408-chr6:13709684..13713261,5	MCF-7	breast:
4	chr6:13572710..13576955-chr6:13610549..13618685,22	MCF-7	breast:
5	chr6:13326831..13329117-chr6:13574155..13576632,2	K562	blood:
6	chr6:13484642..13487748-chr6:13572714..13576594,3	K562	blood:
7	chr6:13573058..13574612-chr6:13812488..13814819,2	MCF-7	breast:
8	chr6:13573221..13576787-chr6:13710917..13713733,6	K562	blood:
9	chr3:129032834..129033727-chr6:13574050..13574658,2	Hela-S3	cervix:
10	chr21:46821773..46824180-chr6:13571587..13574488,2	MCF-7	breast:
11	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
12	chr6:13397579..13400126-chr6:13573111..13574727,2	MCF-7	breast:
13	chr6:13571943..13574615-chr6:13703735..13706256,3	K562	blood:
14	chr4:99850217..99850807-chr6:13574209..13575136,2	Hela-S3	cervix:
15	chr6:13573004..13578027-chr6:13613856..13617870,10	MCF-7	breast:
16	chr6:13571943..13574615-chr6:13703735..13705553,2	K562	blood:
17	chr6:13572493..13576795-chr6:13677578..13681816,6	K562	blood:
18	chr6:13406137..13408577-chr6:13573927..13576170,2	MCF-7	breast:
19	chr6:13572923..13577086-chr6:13614342..13617597,6	K562	blood:
20	chr6:13573217..13575552-chr6:13711779..13713289,2	K562	blood:
21	chr6:13572531..13574981-chr6:13813241..13815537,2	K562	blood:
22	chr6:13574305..13575294-chr8:103665947..103666716,2	Hela-S3	cervix:
23	chr6:13572776..13574707-chr6:13619444..13621662,2	MCF-7	breast:
24	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
25	chr6:13572897..13576165-chr6:13620913..13622919,3	K562	blood:
26	chr17:57915194..57915741-chr6:13574211..13574814,2	Hela-S3	cervix:
27	chr6:13274197..13275936-chr6:13573987..13576342,2	K562	blood:
28	chr6:13574068..13574860-chr6:13615468..13616038,2	K562	blood:
29	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
30	chr6:13572865..13577994-chr6:13612366..13619020,17	K562	blood:
31	chr6:13280798..13285135-chr6:13573249..13575552,3	K562	blood:
32	chr6:13327393..13331113-chr6:13573725..13577168,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RANBP9-2	chr6:13572305-13574446	NONHSAT107810

Variant related genes	Relation type
SIRT5	TF binding region
SIRT5	CpG island
ENSG00000268059	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000252966	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000272379	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000050393	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11753306	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328676	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804910	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804911	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804914	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804916	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804917	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804919	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804920	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804922	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804925	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2804926	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2804927	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841505	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2841506	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841507	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841508	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2841509	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2841511	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712037	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2804924	SIRT5	cis	Thyroid	GTEx

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	chr6:13573600-13574400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:13573600-13574400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr6:13573600-13575600	Active TSS	Right Ventricle	heart
5	chr6:13573800-13574400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr6:13573800-13574400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:13573800-13574400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:13573800-13574400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:13573800-13574400	Enhancers	Small Intestine	intestine
10	chr6:13573800-13574400	Enhancers	Spleen	Spleen
11	chr6:13573800-13574400	Flanking Active TSS	Dnd41	blood
12	chr6:13573800-13575000	Active TSS	Fetal Muscle Trunk	muscle
13	chr6:13573800-13575600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:13573800-13575600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:13573800-13575600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:13573800-13575600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:13573800-13575600	Active TSS	Brain Angular Gyrus	brain
18	chr6:13573800-13575600	Active TSS	Psoas Muscle	Psoas
19	chr6:13573800-13575800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:13573800-13575800	Active TSS	Brain Germinal Matrix	brain
21	chr6:13574000-13574400	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr6:13574000-13574400	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr6:13574000-13574400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr6:13574000-13574400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:13574000-13574400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr6:13574000-13574400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:13574000-13574400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:13574000-13574400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:13574000-13574400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:13574000-13574400	Flanking Active TSS	Fetal Thymus	thymus
31	chr6:13574000-13575200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:13574000-13575400	Active TSS	Lung	lung
33	chr6:13574000-13575600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:13574000-13575600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:13574000-13575600	Active TSS	Aorta	Aorta
36	chr6:13574000-13575600	Active TSS	Colon Smooth Muscle	Colon
37	chr6:13574000-13575600	Active TSS	Gastric	stomach
38	chr6:13574000-13575600	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:13574000-13575600	Transcr. at gene 5' and 3'	Right Atrium	heart
40	chr6:13574000-13575600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr6:13574000-13575600	Active TSS	NHDF-Ad	bronchial
42	chr6:13574000-13575600	Active TSS	NHLF	lung
43	chr6:13574000-13575800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:13574000-13575800	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr6:13574000-13575800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:13574000-13575800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr6:13574000-13575800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:13574000-13575800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:13574000-13575800	Active TSS	Fetal Brain Female	brain
50	chr6:13574000-13576000	Active TSS	HUES64 Cell Line	embryonic stem cell

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