Variant report

Variant	rs3095290
Chromosome Location	chr6:29641637-29641638
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	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs2535238	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535274	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2535275	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747421	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747427	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747428	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747429	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747460	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2907897	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs29218	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29228	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094579	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094724	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3094725	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3095266	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095269	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3095271	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095284	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3095294	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3116814	0.82[ASN][1000 genomes]
rs3117289	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117295	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3117299	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3117301	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3117312	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3117318	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129033	0.82[ASN][1000 genomes]
rs3129035	0.82[ASN][1000 genomes]
rs3129036	0.81[EUR][1000 genomes]
rs3129039	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129058	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129062	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129063	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129069	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129073	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129084	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3129092	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3129189	0.81[AMR][1000 genomes]
rs3130251	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3131889	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3131895	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131898	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs374317	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs375248	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs375984	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs376319	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387640	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387642	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs417764	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448380	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448489	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258017	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3095290	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3095290	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs3095290	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3095290	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29634600-29642000	Weak transcription	Brain Angular Gyrus	brain
4	chr6:29636400-29643800	Weak transcription	Fetal Heart	heart
5	chr6:29636600-29642000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:29636600-29644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:29637000-29644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:29638800-29644400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:29639800-29643400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:29640600-29643800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:29640800-29643000	Weak transcription	NHEK	skin
13	chr6:29641600-29642000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:29641600-29643000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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