Variant report

Variant	rs33932084
Chromosome Location	chr6:28268824-28268825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28265086..28267081-chr6:28267676..28269860,3	K562	blood:
2	chr6:28268157..28273166-chr6:28302896..28306229,5	K562	blood:
3	chr6:28268084..28270649-chr6:28302585..28305878,5	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	0.93[EUR][1000 genomes]
rs13191038	0.84[EUR][1000 genomes]
rs13191786	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13195291	0.91[EUR][1000 genomes]
rs13197574	0.84[EUR][1000 genomes]
rs13197633	0.91[EUR][1000 genomes]
rs13198809	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13201308	0.84[EUR][1000 genomes]
rs13201681	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13203816	0.84[EUR][1000 genomes]
rs13204012	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13205211	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13205911	0.84[EUR][1000 genomes]
rs13207345	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13208096	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13211507	0.98[EUR][1000 genomes]
rs13213152	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13213986	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13214023	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13217619	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13217984	0.84[EUR][1000 genomes]
rs17720293	0.80[EUR][1000 genomes]
rs2232423	0.87[EUR][1000 genomes]
rs2232426	0.87[EUR][1000 genomes]
rs2232429	0.87[EUR][1000 genomes]
rs34166054	0.84[EUR][1000 genomes]
rs34218844	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34243448	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34371502	0.84[EUR][1000 genomes]
rs34396849	0.98[EUR][1000 genomes]
rs34505829	0.84[EUR][1000 genomes]
rs34546986	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34588114	0.84[EUR][1000 genomes]
rs34661125	0.98[EUR][1000 genomes]
rs34676049	0.91[EUR][1000 genomes]
rs34691223	0.98[EUR][1000 genomes]
rs34765154	0.84[EUR][1000 genomes]
rs34832585	0.84[EUR][1000 genomes]
rs34871267	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34878803	0.98[EUR][1000 genomes]
rs34950484	0.98[EUR][1000 genomes]
rs35001169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35016036	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35017208	0.91[EUR][1000 genomes]
rs35030260	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35072899	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35098436	0.84[EUR][1000 genomes]
rs35345226	0.84[EUR][1000 genomes]
rs35353359	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35656932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35744819	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35749575	0.84[EUR][1000 genomes]
rs35781323	0.84[EUR][1000 genomes]
rs35883476	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35902873	0.84[EUR][1000 genomes]
rs36092177	0.87[EUR][1000 genomes]
rs55690788	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56075693	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56189111	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66886492	0.84[EUR][1000 genomes]
rs67297533	0.81[EUR][1000 genomes]
rs67340775	0.96[EUR][1000 genomes]
rs67381177	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67981811	0.87[EUR][1000 genomes]
rs67998226	0.98[EUR][1000 genomes]
rs71559070	0.84[EUR][1000 genomes]
rs71559072	0.84[EUR][1000 genomes]
rs72846780	0.84[EUR][1000 genomes]
rs72846794	0.84[EUR][1000 genomes]
rs72854513	0.85[AMR][1000 genomes];0.98[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
rs33932084	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs33932084	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs33932084	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs33932084	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
7	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
9	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
11	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
17	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
18	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
20	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:28255400-28278400	Weak transcription	HepG2	liver
23	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
24	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:28256400-28271600	Weak transcription	Liver	Liver
26	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
29	chr6:28257800-28279000	Weak transcription	HMEC	breast
30	chr6:28258000-28270800	Weak transcription	NH-A	brain
31	chr6:28258400-28269600	Weak transcription	Fetal Kidney	kidney
32	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain
34	chr6:28263200-28270200	Strong transcription	Brain Germinal Matrix	brain
35	chr6:28263400-28269400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:28264200-28273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:28264200-28273000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:28264400-28270000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:28264400-28270200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:28264400-28270400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr6:28264600-28270000	Strong transcription	Adipose Nuclei	Adipose
42	chr6:28264600-28270000	Strong transcription	Fetal Brain Female	brain
43	chr6:28264800-28272000	Weak transcription	HSMM	muscle
44	chr6:28264800-28274200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:28264800-28278600	Weak transcription	Fetal Intestine Small	intestine
46	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:28265400-28269000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:28265400-28271400	Weak transcription	NHLF	lung
49	chr6:28265400-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:28265600-28274000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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