Variant report

Variant	rs962899
Chromosome Location	chr6:30226811-30226812
allele	C/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	PML	chr6:30226802-30228247	GM12878	blood:	n/a	chr6:30227303-30227311
2	POLR2A	chr6:30226787-30228459	GM12878	blood:	n/a	n/a
3	RFX5	chr6:30226110-30228388	H1-hESC	embryonic stem cell:	n/a	chr6:30227308-30227317
4	RFX5	chr6:30225760-30229308	IMR90	lung:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
5	RFX5	chr6:30225288-30228368	SK-N-SH	brain:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
6	CREB1	chr6:30226763-30227821	GM12878	blood:	n/a	n/a
7	MTA3	chr6:30226778-30228206	GM12878	blood:	n/a	n/a
8	NFIC	chr6:30226762-30227600	GM12878	blood:	n/a	n/a
9	NFYB	chr6:30226665-30227548	GM12878	blood:	n/a	chr6:30227305-30227318 chr6:30227302-30227317 chr6:30227305-30227320 chr6:30227307-30227317 chr6:30227305-30227319 chr6:30227305-30227320
10	RFX5	chr6:30226775-30227870	GM12878	blood:	n/a	chr6:30227308-30227317
11	RFX5	chr6:30226569-30227909	HepG2	liver:	n/a	chr6:30227308-30227317
12	MAZ	chr6:30226291-30228294	IMR90	lung:	n/a	n/a
13	CREB1	chr6:30226795-30227979	HepG2	liver:	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
ENSG00000241370	Chromatin interaction
ENSG00000231074	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]
rs2516713	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]
rs974963	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs962899	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs962899	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30225800-30227000	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr6:30226000-30227000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:30226000-30227000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:30226000-30227000	Enhancers	Pancreas	Pancrea
5	chr6:30226000-30227200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:30226000-30227200	Enhancers	Small Intestine	intestine
7	chr6:30226200-30227000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:30226200-30227000	Weak transcription	Spleen	Spleen
9	chr6:30226600-30227000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:30226600-30228000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:30226600-30229000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr6:30226800-30227000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:30226800-30227000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
14	chr6:30226800-30227000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:30226800-30227000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:30226800-30227000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr6:30226800-30227000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:30226800-30227000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:30226800-30227000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:30226800-30227000	Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:30226800-30227000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr6:30226800-30227000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:30226800-30227000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:30226800-30227000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:30226800-30227000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:30226800-30227000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:30226800-30227000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:30226800-30227000	Enhancers	Liver	Liver
29	chr6:30226800-30227000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
30	chr6:30226800-30227000	Enhancers	Esophagus	oesophagus
31	chr6:30226800-30227000	Enhancers	Fetal Kidney	kidney
32	chr6:30226800-30227000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr6:30226800-30227000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr6:30226800-30227000	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr6:30226800-30227000	Enhancers	Placenta	Placenta
36	chr6:30226800-30227000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
37	chr6:30226800-30227000	Enhancers	Right Ventricle	heart
38	chr6:30226800-30227000	Enhancers	HSMMtube	muscle
39	chr6:30226800-30227000	Enhancers	NHDF-Ad	bronchial
40	chr6:30226800-30227200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:30226800-30227200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:30226800-30227200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr6:30226800-30227200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:30226800-30227200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
45	chr6:30226800-30227200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:30226800-30227200	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr6:30226800-30227200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr6:30226800-30227200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr6:30226800-30227200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:30226800-30227200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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