Variant report

Variant	rs1045251
Chromosome Location	chr6:30259657-30259658
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30252759..30255238-chr6:30259502..30262468,2	MCF-7	breast:
2	chr6:30259621..30261332-chr6:30272823..30275390,2	K562	blood:
3	chr6:30258650..30265091-chr6:30270138..30274799,6	MCF-7	breast:
4	chr6:30254447..30256446-chr6:30257313..30259885,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM39-1	chr6:30259314-30260239	XLOC_005238

Variant related genes	Relation type
ENSG00000231074	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1060065	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1075105	0.80[AFR][1000 genomes]
rs1264616	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264619	0.80[AFR][1000 genomes]
rs1473102	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1579218	0.80[ASN][1000 genomes]
rs1579219	0.80[ASN][1000 genomes]
rs2023476	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2023477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2023478	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057727	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074474	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285798	0.82[ASN][1000 genomes]
rs2394779	0.83[ASN][1000 genomes]
rs2394780	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2508026	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516697	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516699	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516700	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516702	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516704	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516705	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516706	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516707	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516710	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516713	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516718	0.83[AFR][1000 genomes]
rs2516719	0.82[AFR][1000 genomes]
rs2523737	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523744	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523745	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523746	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523747	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523748	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2523750	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261943	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs261948	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs261949	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28360021	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360023	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844752	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844763	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844765	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894145	0.81[ASN][1000 genomes]
rs3778624	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778626	0.81[ASN][1000 genomes]
rs6904208	0.82[AFR][1000 genomes]
rs6912239	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912495	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7452694	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767817	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295843	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295844	0.83[ASN][1000 genomes]
rs9357095	0.83[ASN][1000 genomes]
rs9366755	0.82[ASN][1000 genomes]
rs9368628	0.83[ASN][1000 genomes]
rs9368632	0.83[ASN][1000 genomes]
rs9368633	0.83[ASN][1000 genomes]
rs9380168	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380174	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9391679	0.83[ASN][1000 genomes]
rs9391806	0.83[ASN][1000 genomes]
rs9391807	0.83[ASN][1000 genomes]
rs9393999	0.83[ASN][1000 genomes]
rs9394000	0.83[ASN][1000 genomes]
rs9394001	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394002	0.81[ASN][1000 genomes]
rs9394003	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs962899	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974963	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1045251	LOC401245	cis	multi-tissue	Pritchard
rs1045251	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs1045251	HCG18	cis	normal skin	skin_eQTL
rs1045251	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30247600-30262400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:30252200-30262600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr6:30255200-30259800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:30255200-30261000	Weak transcription	Fetal Brain Male	brain
5	chr6:30255600-30261200	Weak transcription	Stomach Mucosa	stomach
6	chr6:30255600-30264000	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:30255800-30260200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:30255800-30261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:30255800-30264400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:30256000-30260200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr6:30256000-30263200	Strong transcription	HSMMtube	muscle
12	chr6:30256000-30270200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:30256200-30259800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
14	chr6:30256200-30259800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
15	chr6:30256200-30261200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr6:30256200-30262800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr6:30256200-30263800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:30256200-30264000	Strong transcription	Brain Anterior Caudate	brain
19	chr6:30256200-30264800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:30256200-30292000	Weak transcription	Fetal Heart	heart
21	chr6:30256400-30263200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr6:30256400-30263200	Strong transcription	Thymus	Thymus
23	chr6:30256400-30263400	Strong transcription	Left Ventricle	heart
24	chr6:30256400-30263800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:30256400-30263800	Strong transcription	Fetal Intestine Large	intestine
26	chr6:30256400-30264000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr6:30256400-30264200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:30256400-30264200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:30256400-30264400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:30256600-30263600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr6:30256600-30263800	Strong transcription	A549	lung
32	chr6:30256600-30264200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr6:30256800-30259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:30256800-30263200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:30256800-30263800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:30256800-30264400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:30257000-30261600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:30257000-30262200	Weak transcription	Hela-S3	cervix
39	chr6:30257000-30263800	Strong transcription	Primary B cells from cord blood	blood
40	chr6:30257000-30264000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:30257000-30264000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:30257000-30264000	Strong transcription	Placenta	Placenta
43	chr6:30257000-30264200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:30257000-30264200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:30257000-30264200	Strong transcription	Fetal Stomach	stomach
46	chr6:30257000-30264200	Strong transcription	NH-A	brain
47	chr6:30257000-30264400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:30257000-30264400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:30257000-30264400	Strong transcription	Fetal Thymus	thymus
50	chr6:30257200-30259800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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