Variant report

Variant	rs2247429
Chromosome Location	chr6:146217769-146217770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146134473..146136015-chr6:146217763..146219719,2	MCF-7	breast:
2	chr6:146056598..146058276-chr6:146215722..146218388,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO30-2	chr6:146216172-146218558	NONHSAT115417

Variant related genes	Relation type
ENSG00000270638	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000112425	Chromatin interaction

Extended variants
information (count: 173 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:170)

rs_ID	r²[population]
rs10223508	0.91[EUR][1000 genomes]
rs10457792	0.80[AMR][1000 genomes]
rs10457793	0.82[AMR][1000 genomes]
rs10457794	0.82[AMR][1000 genomes]
rs10457795	0.80[AMR][1000 genomes]
rs1062067	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1062068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872580	0.82[ASN][1000 genomes]
rs11155452	0.80[AMR][1000 genomes]
rs1133832	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11755334	0.82[AMR][1000 genomes]
rs11760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12194437	0.82[AMR][1000 genomes]
rs12199362	0.82[ASN][1000 genomes]
rs13198450	0.83[ASN][1000 genomes]
rs1331636	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1331637	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1412081	0.80[AMR][1000 genomes]
rs1415746	0.81[ASN][1000 genomes]
rs1415747	0.81[ASN][1000 genomes]
rs1832362	0.82[EUR][1000 genomes]
rs1890171	0.82[ASN][1000 genomes]
rs1986729	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2050027	0.81[ASN][1000 genomes]
rs2073287	0.80[EUR][1000 genomes]
rs2144477	0.80[AMR][1000 genomes]
rs2207785	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2224120	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2224121	0.83[EUR][1000 genomes]
rs2243665	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2246334	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247206	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2247211	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2247317	0.89[EUR][1000 genomes]
rs2247666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249147	0.82[EUR][1000 genomes]
rs2249386	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250387	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2253194	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253307	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253654	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253764	0.86[EUR][1000 genomes]
rs2253768	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2253880	0.86[EUR][1000 genomes]
rs2253886	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253887	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2254257	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254283	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2254288	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2256998	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265467	0.89[EUR][1000 genomes]
rs2265468	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265469	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2265471	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2265472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2265474	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2265477	0.89[EUR][1000 genomes]
rs2265915	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2265916	0.82[EUR][1000 genomes]
rs2265917	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2265918	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2265919	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2328709	0.82[ASN][1000 genomes]
rs2328712	0.83[EUR][1000 genomes]
rs2474356	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2485632	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2492855	0.83[EUR][1000 genomes]
rs2748482	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2748483	0.83[EUR][1000 genomes]
rs2748484	0.83[EUR][1000 genomes]
rs2748485	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2748499	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748502	0.84[EUR][1000 genomes]
rs2777476	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2777477	0.84[EUR][1000 genomes]
rs2777484	0.83[EUR][1000 genomes]
rs2814866	0.83[EUR][1000 genomes]
rs2814867	0.82[EUR][1000 genomes]
rs2814869	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2814874	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2814875	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2814876	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2814877	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2814879	0.86[EUR][1000 genomes]
rs2814880	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3811102	0.82[ASN][1000 genomes]
rs3923579	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924498	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924499	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924502	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075694	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075695	0.84[EUR][1000 genomes]
rs4075696	0.84[EUR][1000 genomes]
rs4243478	0.83[EUR][1000 genomes]
rs4280983	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4314514	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4316025	0.86[EUR][1000 genomes]
rs4360151	0.93[EUR][1000 genomes]
rs4391282	0.91[EUR][1000 genomes]
rs4435956	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4566902	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4895683	0.81[ASN][1000 genomes]
rs4896844	0.81[ASN][1000 genomes]
rs4896852	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56181683	0.85[EUR][1000 genomes]
rs62435810	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570713	0.81[ASN][1000 genomes]
rs6570715	0.81[ASN][1000 genomes]
rs6570717	0.81[ASN][1000 genomes]
rs6570719	0.81[ASN][1000 genomes]
rs6570723	0.82[EUR][1000 genomes]
rs6570724	0.82[EUR][1000 genomes]
rs6570736	0.83[AMR][1000 genomes]
rs6906258	0.82[ASN][1000 genomes]
rs6906402	0.82[ASN][1000 genomes]
rs6910790	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6914813	0.80[AMR][1000 genomes]
rs6915718	0.82[ASN][1000 genomes]
rs6917135	0.82[EUR][1000 genomes]
rs6917482	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6922507	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923545	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6924159	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6926076	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6926657	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6931553	0.82[ASN][1000 genomes]
rs6938972	0.80[AMR][1000 genomes]
rs7742333	0.81[EUR][1000 genomes]
rs7745696	0.82[EUR][1000 genomes]
rs7747576	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7752286	0.81[ASN][1000 genomes]
rs7753092	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753696	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755440	0.81[AMR][1000 genomes]
rs7762562	0.82[EUR][1000 genomes]
rs854145	0.80[EUR][1000 genomes]
rs864390	0.84[EUR][1000 genomes]
rs866473	0.81[ASN][1000 genomes]
rs9322043	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322047	0.81[AMR][1000 genomes]
rs932522	0.83[ASN][1000 genomes]
rs9373475	0.82[ASN][1000 genomes]
rs9373485	0.81[AMR][1000 genomes]
rs9376968	0.82[EUR][1000 genomes]
rs9376970	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9376971	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9376975	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9386132	0.82[ASN][1000 genomes]
rs9386134	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9386141	0.92[EUR][1000 genomes]
rs9390355	0.81[ASN][1000 genomes]
rs9390356	0.82[ASN][1000 genomes]
rs9390365	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390377	0.81[AMR][1000 genomes]
rs9399567	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9399569	0.92[EUR][1000 genomes]
rs9399571	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9403749	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403750	0.81[EUR][1000 genomes]
rs9403755	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9403756	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403757	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9403764	0.83[ASN][1000 genomes]
rs9497424	0.97[EUR][1000 genomes]
rs9497425	0.95[EUR][1000 genomes]
rs9497427	0.94[EUR][1000 genomes]
rs9497431	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9497434	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9497435	0.92[EUR][1000 genomes]
rs9791313	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv437525	chr6:146212285-146230454	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2247429	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146188000-146218800	Weak transcription	Right Ventricle	heart
2	chr6:146196600-146219600	Weak transcription	HMEC	breast
3	chr6:146197800-146219600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:146198200-146218600	Weak transcription	Fetal Heart	heart
5	chr6:146198200-146225600	Weak transcription	HSMMtube	muscle
6	chr6:146200400-146228600	Weak transcription	Pancreas	Pancrea
7	chr6:146201200-146225600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:146201200-146230400	Weak transcription	NHEK	skin
9	chr6:146201800-146219600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:146202800-146220000	Weak transcription	Thymus	Thymus
11	chr6:146203200-146219600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:146203400-146218600	Weak transcription	A549	lung
13	chr6:146204800-146224800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:146206800-146219600	Weak transcription	Fetal Intestine Small	intestine
15	chr6:146207800-146240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:146208000-146219000	Weak transcription	Small Intestine	intestine
17	chr6:146208400-146218000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:146208400-146218800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:146208800-146230000	Weak transcription	Colonic Mucosa	Colon
20	chr6:146209800-146219000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:146210200-146219800	Weak transcription	Gastric	stomach
22	chr6:146210200-146231000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:146210400-146218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:146210400-146218800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:146210400-146218800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:146210400-146219600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:146210400-146219600	Weak transcription	Lung	lung
28	chr6:146210400-146219800	Weak transcription	Esophagus	oesophagus
29	chr6:146210400-146221600	Weak transcription	Psoas Muscle	Psoas
30	chr6:146210400-146230400	Weak transcription	NH-A	brain
31	chr6:146210400-146282000	Weak transcription	Spleen	Spleen
32	chr6:146211000-146218800	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:146211200-146218400	Weak transcription	Fetal Brain Male	brain
34	chr6:146211200-146224800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:146211600-146236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr6:146212400-146219800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:146212800-146218600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:146212800-146218600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:146212800-146219600	Weak transcription	Aorta	Aorta
40	chr6:146212800-146219600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:146212800-146226000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:146213000-146218600	Weak transcription	Brain Angular Gyrus	brain
43	chr6:146213000-146218800	Weak transcription	NHLF	lung
44	chr6:146213200-146218800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:146213200-146218800	Weak transcription	Fetal Lung	lung
46	chr6:146213200-146221000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:146213400-146218600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:146213600-146218800	Weak transcription	HepG2	liver
49	chr6:146213600-146219000	Weak transcription	Primary T cells from cord blood	blood
50	chr6:146213800-146225000	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links