Variant report

Variant	rs2516713
Chromosome Location	chr6:30227246-30227247
allele	A/T
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	BHLHE40	chr6:30227101-30227442	GM12878	blood:	n/a	n/a
2	PML	chr6:30226802-30228247	GM12878	blood:	n/a	chr6:30227303-30227311
3	TBP	chr6:30227003-30227566	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:30227102-30227985	MCF-7	breast:	n/a	n/a
5	POLR2A	chr6:30226787-30228459	GM12878	blood:	n/a	n/a
6	CHD1	chr6:30226846-30228493	IMR90	lung:	n/a	chr6:30228097-30228107 chr6:30228006-30228013
7	ZBTB7A	chr6:30226876-30227318	HepG2	liver:	n/a	n/a
8	ELF1	chr6:30226857-30228371	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:30227013-30227667	SK-N-MC	brain:	n/a	n/a
10	CEBPB	chr6:30227144-30227750	IMR90	lung:	n/a	chr6:30227308-30227316
11	POLR2A	chr6:30227057-30227522	H1-hESC	embryonic stem cell:	n/a	n/a
12	E2F6	chr6:30226971-30228552	H1-hESC	embryonic stem cell:	n/a	chr6:30228006-30228013 chr6:30228058-30228070
13	TBP	chr6:30227037-30227502	GM12878	blood:	n/a	n/a
14	POU2F2	chr6:30227192-30227564	GM12891	blood:	n/a	n/a
15	RFX5	chr6:30226110-30228388	H1-hESC	embryonic stem cell:	n/a	chr6:30227308-30227317
16	RFX5	chr6:30227079-30227442	K562	blood:	n/a	chr6:30227308-30227317
17	ZNF143	chr6:30227077-30227424	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr6:30226905-30227402	GM19099	blood:	n/a	n/a
19	POLR2A	chr6:30227208-30227564	GM10847	blood:	n/a	n/a
20	CHD2	chr6:30227097-30227421	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP1	chr6:30227069-30227456	GM12878	blood:	n/a	chr6:30227272-30227293
22	FOS	chr6:30227128-30227299	MCF10A-Er-Src	breast:	n/a	n/a
23	MYBL2	chr6:30226880-30227720	HepG2	liver:	n/a	n/a
24	SIN3A	chr6:30227060-30227424	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOSL2	chr6:30226972-30227602	HepG2	liver:	n/a	chr6:30227287-30227301 chr6:30227309-30227318
26	POLR2A	chr6:30226966-30228031	GM12891	blood:	n/a	n/a
27	CREB1	chr6:30226940-30227492	ECC-1	luminal epithelium:	n/a	n/a
28	RELA	chr6:30226971-30227568	GM18951	blood:	n/a	n/a
29	CEBPD	chr6:30227032-30227578	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:30226962-30227691	GM12878	blood:	n/a	n/a
31	RFX5	chr6:30225760-30229308	IMR90	lung:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
32	TAF1	chr6:30227159-30227586	H1-hESC	embryonic stem cell:	n/a	n/a
33	ELF1	chr6:30226993-30227484	HepG2	liver:	n/a	n/a
34	MAX	chr6:30227123-30227530	SK-N-SH	brain:	n/a	n/a
35	ELF1	chr6:30226979-30227533	MCF-7	breast:	n/a	n/a
36	POLR2A	chr6:30226956-30227540	GM12891	blood:	n/a	n/a
37	CREB1	chr6:30226982-30227524	H1-hESC	embryonic stem cell:	n/a	n/a
38	EBF1	chr6:30227041-30227438	GM12878	blood:	n/a	n/a
39	POU2F2	chr6:30227240-30227700	GM12878	blood:	n/a	n/a
40	MAX	chr6:30227026-30227512	GM12878	blood:	n/a	n/a
41	ELF1	chr6:30226942-30227529	MCF-7	breast:	n/a	n/a
42	RFX5	chr6:30225288-30228368	SK-N-SH	brain:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
43	POLR2A	chr6:30226980-30227563	GM12891	blood:	n/a	n/a
44	RCOR1	chr6:30227078-30227373	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:30227027-30227568	HepG2	liver:	n/a	n/a
46	NFYA	chr6:30227002-30227394	GM12878	blood:	n/a	chr6:30227305-30227318 chr6:30227305-30227320 chr6:30227307-30227317 chr6:30227305-30227319 chr6:30227305-30227320
47	POLR2A	chr6:30227134-30227596	MCF-7	breast:	n/a	n/a
48	BHLHE40	chr6:30227058-30227433	HepG2	liver:	n/a	n/a
49	IRF3	chr6:30227146-30227405	GM12878	blood:	n/a	n/a
50	FOS	chr6:30227111-30227293	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30226094..30227681-chr6:30293299..30296159,2	MCF-7	breast:
2	chr6:30225449..30228967-chr6:30292795..30296377,4	K562	blood:
3	chr6:30226682..30228906-chr6:30311932..30314057,2	MCF-7	breast:
4	chr6:30225542..30228363-chr6:30311426..30313496,2	MCF-7	breast:

Variant related genes	Relation type
HLA-L	TF binding region
ENSG00000270604	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204599	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1045251	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1060065	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1264616	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473102	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2023476	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023477	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057727	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074474	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2097773	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394779	0.80[ASN][1000 genomes]
rs2394780	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508026	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516697	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516701	0.86[AFR][1000 genomes]
rs2516702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516706	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516707	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516718	0.90[AFR][1000 genomes]
rs2516719	0.89[AFR][1000 genomes]
rs2523737	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523747	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523748	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523750	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261943	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261948	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261949	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28360023	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844752	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844761	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844763	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844765	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778624	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6912239	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6912495	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7452694	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767817	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295843	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295844	0.81[ASN][1000 genomes]
rs9357095	0.80[ASN][1000 genomes]
rs9368628	0.80[ASN][1000 genomes]
rs9368632	0.80[ASN][1000 genomes]
rs9368633	0.80[ASN][1000 genomes]
rs9380168	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380174	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391679	0.80[ASN][1000 genomes]
rs9391806	0.80[ASN][1000 genomes]
rs9391807	0.80[ASN][1000 genomes]
rs9393999	0.80[ASN][1000 genomes]
rs9394000	0.80[ASN][1000 genomes]
rs9394001	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394003	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs962899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974963	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2516713	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs2516713	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30226600-30228000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30226600-30229000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:30226800-30227400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr6:30226800-30227600	Active TSS	Fetal Brain Female	brain
5	chr6:30226800-30227800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr6:30226800-30227800	Active TSS	Stomach Smooth Muscle	stomach
7	chr6:30226800-30228000	Active TSS	Right Atrium	heart
8	chr6:30226800-30228200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:30226800-30228200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:30226800-30228200	Active TSS	Brain Anterior Caudate	brain
11	chr6:30226800-30228200	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:30226800-30228200	Active TSS	A549	lung
13	chr6:30226800-30228400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:30226800-30228400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:30226800-30228400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr6:30226800-30228400	Active TSS	HSMM	muscle
17	chr6:30226800-30228600	Enhancers	Fetal Brain Male	brain
18	chr6:30226800-30228600	Enhancers	Fetal Heart	heart
19	chr6:30226800-30228800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:30227000-30227400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:30227000-30227400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:30227000-30227400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:30227000-30227400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr6:30227000-30227400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:30227000-30227400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr6:30227000-30227400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr6:30227000-30227400	Flanking Active TSS	Thymus	Thymus
28	chr6:30227000-30227600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:30227000-30227600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:30227000-30227600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:30227000-30227600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:30227000-30227600	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr6:30227000-30227600	Bivalent/Poised TSS	NHEK	skin
34	chr6:30227000-30227800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:30227000-30227800	Active TSS	Primary B cells from cord blood	blood
36	chr6:30227000-30227800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr6:30227000-30227800	Active TSS	Fetal Lung	lung
38	chr6:30227000-30227800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
39	chr6:30227000-30228000	Active TSS	Fetal Kidney	kidney
40	chr6:30227000-30228000	Active TSS	Gastric	stomach
41	chr6:30227000-30228000	Active TSS	Right Ventricle	heart
42	chr6:30227000-30228000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr6:30227000-30228200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr6:30227000-30228200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:30227000-30228200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:30227000-30228200	Active TSS	Aorta	Aorta
47	chr6:30227000-30228200	Flanking Active TSS	Liver	Liver
48	chr6:30227000-30228200	Active TSS	Colonic Mucosa	Colon
49	chr6:30227000-30228200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:30227000-30228200	Active TSS	Ovary	ovary

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