Variant report

Variant	rs34661125
Chromosome Location	chr6:28281894-28281895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28278749..28286420-chr6:28298924..28309589,20	K562	blood:
2	chr6:28263544..28266110-chr6:28280477..28282083,2	K562	blood:
3	chr6:28280348..28282380-chr6:28284969..28286632,2	K562	blood:
4	chr6:28280497..28286248-chr6:28302122..28306954,10	K562	blood:
5	chr6:28281200..28284127-chr6:28290711..28292363,2	K562	blood:
6	chr6:28281200..28284924-chr6:28289065..28292211,3	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs13190888	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13191038	0.85[EUR][1000 genomes]
rs13191786	1.00[EUR][1000 genomes]
rs13195291	0.93[EUR][1000 genomes]
rs13197574	0.85[EUR][1000 genomes]
rs13197633	0.93[EUR][1000 genomes]
rs13198809	0.93[EUR][1000 genomes]
rs13201308	0.85[EUR][1000 genomes]
rs13201681	0.93[EUR][1000 genomes]
rs13203816	0.85[EUR][1000 genomes]
rs13204012	1.00[EUR][1000 genomes]
rs13205211	1.00[EUR][1000 genomes]
rs13205911	0.85[EUR][1000 genomes]
rs13207345	1.00[EUR][1000 genomes]
rs13208096	1.00[EUR][1000 genomes]
rs13211507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213152	0.93[EUR][1000 genomes]
rs13213986	0.89[EUR][1000 genomes]
rs13214023	0.93[EUR][1000 genomes]
rs13217619	0.93[EUR][1000 genomes]
rs13217984	0.85[EUR][1000 genomes]
rs2232423	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232426	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232429	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33932084	0.98[EUR][1000 genomes]
rs34166054	0.85[EUR][1000 genomes]
rs34218844	1.00[EUR][1000 genomes]
rs34243448	1.00[EUR][1000 genomes]
rs34371502	0.85[EUR][1000 genomes]
rs34396849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34505829	0.85[EUR][1000 genomes]
rs34546986	0.89[EUR][1000 genomes]
rs34588114	0.85[EUR][1000 genomes]
rs34676049	0.93[EUR][1000 genomes]
rs34691223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34765154	0.85[EUR][1000 genomes]
rs34832585	0.85[EUR][1000 genomes]
rs34871267	0.89[EUR][1000 genomes]
rs34878803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34950484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35001169	0.93[EUR][1000 genomes]
rs35016036	0.96[EUR][1000 genomes]
rs35017208	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35030260	0.98[EUR][1000 genomes]
rs35072899	1.00[EUR][1000 genomes]
rs35098436	0.85[EUR][1000 genomes]
rs35345226	0.85[EUR][1000 genomes]
rs35353359	0.93[EUR][1000 genomes]
rs35656932	0.93[EUR][1000 genomes]
rs35744819	0.93[EUR][1000 genomes]
rs35749575	0.85[EUR][1000 genomes]
rs35781323	0.85[EUR][1000 genomes]
rs35883476	0.89[EUR][1000 genomes]
rs35902873	0.85[EUR][1000 genomes]
rs36092177	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55690788	0.93[EUR][1000 genomes]
rs56075693	1.00[EUR][1000 genomes]
rs56189111	1.00[EUR][1000 genomes]
rs66886492	0.85[EUR][1000 genomes]
rs67297533	0.82[EUR][1000 genomes]
rs67340775	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67381177	0.93[EUR][1000 genomes]
rs67981811	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67998226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559070	0.85[EUR][1000 genomes]
rs71559072	0.85[EUR][1000 genomes]
rs72846780	0.85[EUR][1000 genomes]
rs72846794	0.85[EUR][1000 genomes]
rs72854513	1.00[EUR][1000 genomes]
rs7752608	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34661125	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs34661125	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34661125	AL022393.7	cis	Muscle Skeletal	GTEx
rs34661125	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
3	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
6	chr6:28270000-28290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:28270000-28291400	Weak transcription	Ovary	ovary
8	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
10	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
18	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:28279400-28285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:28279400-28290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:28279600-28282200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:28279600-28282600	Weak transcription	K562	blood
24	chr6:28279800-28288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:28281200-28282400	Weak transcription	Aorta	Aorta
26	chr6:28281200-28284400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:28281200-28290800	Weak transcription	Fetal Stomach	stomach
28	chr6:28281200-28290800	Weak transcription	Left Ventricle	heart
29	chr6:28281200-28291600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:28281200-28291600	Weak transcription	Pancreas	Pancrea
31	chr6:28281200-28293600	Weak transcription	Rectal Smooth Muscle	rectum

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