Variant report

Variant	rs1264619
Chromosome Location	chr6:30260019-30260020
allele	C/G
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:

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: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1045251	0.80[AFR][1000 genomes]
rs1075105	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055553	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12192505	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264616	0.80[AFR][1000 genomes]
rs1264617	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2187979	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2428506	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2428507	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2516696	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2516708	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2516715	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2523740	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs261947	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs261948	0.80[AFR][1000 genomes]
rs261949	0.80[AFR][1000 genomes]
rs2844759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844760	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844762	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2844764	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2844766	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4711213	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900042	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6906180	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6912771	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913293	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6924282	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6924453	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6931387	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295842	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357097	0.90[EUR][1000 genomes]
rs9357098	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368635	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380167	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380172	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1264619	LOC401245	cis	multi-tissue	Pritchard
rs1264619	HCG18	cis	normal skin	skin_eQTL
rs1264619	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs1264619	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	chr6:30255200-30261000	Weak transcription	Fetal Brain Male	brain
4	chr6:30255600-30261200	Weak transcription	Stomach Mucosa	stomach
5	chr6:30255600-30264000	Strong transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:30255800-30260200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:30255800-30261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:30255800-30264400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:30256000-30260200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
10	chr6:30256000-30263200	Strong transcription	HSMMtube	muscle
11	chr6:30256000-30270200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:30256200-30261200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr6:30256200-30262800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr6:30256200-30263800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:30256200-30264000	Strong transcription	Brain Anterior Caudate	brain
16	chr6:30256200-30264800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr6:30256200-30292000	Weak transcription	Fetal Heart	heart
18	chr6:30256400-30263200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr6:30256400-30263200	Strong transcription	Thymus	Thymus
20	chr6:30256400-30263400	Strong transcription	Left Ventricle	heart
21	chr6:30256400-30263800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:30256400-30263800	Strong transcription	Fetal Intestine Large	intestine
23	chr6:30256400-30264000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:30256400-30264200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:30256400-30264200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr6:30256400-30264400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:30256600-30263600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr6:30256600-30263800	Strong transcription	A549	lung
29	chr6:30256600-30264200	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr6:30256800-30263200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:30256800-30263800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:30256800-30264400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:30257000-30261600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:30257000-30262200	Weak transcription	Hela-S3	cervix
35	chr6:30257000-30263800	Strong transcription	Primary B cells from cord blood	blood
36	chr6:30257000-30264000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30257000-30264000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:30257000-30264000	Strong transcription	Placenta	Placenta
39	chr6:30257000-30264200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:30257000-30264200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:30257000-30264200	Strong transcription	Fetal Stomach	stomach
42	chr6:30257000-30264200	Strong transcription	NH-A	brain
43	chr6:30257000-30264400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:30257000-30264400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:30257000-30264400	Strong transcription	Fetal Thymus	thymus
46	chr6:30257200-30262600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:30257200-30263000	Strong transcription	HSMM	muscle
48	chr6:30257200-30263000	Strong transcription	Osteobl	bone
49	chr6:30257200-30263200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:30257200-30263400	Strong transcription	Fetal Muscle Trunk	muscle

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