Variant report

Variant	rs2516710
Chromosome Location	chr6:30228230-30228231
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM39-2	chr6:30228174-30228384	NONHSAT108609

Variant related genes	Relation type
ENSG00000241370	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000231074	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]
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]
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
rs2516710	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs2516710	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30226600-30229000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:30226800-30228400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:30226800-30228400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:30226800-30228400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:30226800-30228400	Active TSS	HSMM	muscle
6	chr6:30226800-30228600	Enhancers	Fetal Brain Male	brain
7	chr6:30226800-30228600	Enhancers	Fetal Heart	heart
8	chr6:30226800-30228800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:30227000-30228400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30227000-30228400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr6:30227000-30228400	Active TSS	Psoas Muscle	Psoas
12	chr6:30227000-30228400	Active TSS	NHLF	lung
13	chr6:30227200-30228400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30227200-30228400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:30227200-30228400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:30227200-30228400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:30227200-30228400	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr6:30227200-30228400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:30227200-30228400	Active TSS	Brain Substantia Nigra	brain
20	chr6:30227200-30228400	Active TSS	Colon Smooth Muscle	Colon
21	chr6:30227200-30228400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr6:30227200-30228400	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:30227200-30228600	Active TSS	Primary T cells from cord blood	blood
24	chr6:30227200-30228800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:30227200-30228800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:30227200-30228800	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr6:30227200-30228800	Active TSS	Osteobl	bone
28	chr6:30227400-30228400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:30227400-30228400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:30227400-30228400	Flanking Active TSS	HMEC	breast
31	chr6:30227400-30228600	Active TSS	Hela-S3	cervix
32	chr6:30227600-30228400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:30227600-30228400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:30227600-30228400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr6:30227600-30228400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:30227600-30228400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:30227600-30228400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr6:30227600-30228400	Active TSS	HepG2	liver
39	chr6:30227600-30228400	Flanking Active TSS	HUVEC	blood vessel
40	chr6:30227800-30228400	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr6:30227800-30228400	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr6:30227800-30228400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:30227800-30228400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:30227800-30228400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:30227800-30228400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr6:30227800-30228400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:30227800-30228400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr6:30227800-30228400	Flanking Active TSS	Spleen	Spleen
49	chr6:30227800-30228600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:30227800-30228600	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links