Variant report

Variant	rs11970339
Chromosome Location	chr6:28624894-28624895
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28614745..28616729-chr6:28622760..28625663,2	MCF-7	breast:
2	chr6:28609862..28611937-chr6:28624089..28625940,2	K562	blood:
3	chr6:28582481..28584280-chr6:28624035..28626997,3	K562	blood:
4	chr6:28613173..28620583-chr6:28620759..28628573,15	K562	blood:
5	chr6:28624820..28630084-chr6:28630901..28635993,6	K562	blood:
6	chr6:28623399..28625951-chr6:28639865..28642751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272278	Chromatin interaction
ENSG00000235570	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11963067	0.83[ASN][1000 genomes]
rs11965972	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11966966	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967609	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11970409	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13220637	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16894194	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894197	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901848	0.81[ASN][1000 genomes]
rs1884936	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884937	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394120	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394121	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394122	0.88[EUR][1000 genomes]
rs2893966	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34020953	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34177106	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34388845	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34470113	0.84[EUR][1000 genomes]
rs34556183	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35466817	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35546888	0.83[ASN][1000 genomes]
rs36069097	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36103239	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4121091	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56389860	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61229539	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923110	0.83[ASN][1000 genomes]
rs6941188	0.81[ASN][1000 genomes]
rs7742957	0.81[ASN][1000 genomes]
rs7767008	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11970339	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs11970339	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs11970339	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28616800-28625200	Weak transcription	Colonic Mucosa	Colon
2	chr6:28624600-28625000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:28624600-28625000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
4	chr6:28624600-28625000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:28624600-28625000	Flanking Active TSS	Fetal Brain Female	brain
6	chr6:28624600-28625000	Bivalent Enhancer	HepG2	liver
7	chr6:28624600-28625200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr6:28624600-28625200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:28624600-28625200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:28624600-28625200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:28624600-28625400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:28624600-28625600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr6:28624600-28625600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:28624600-28626600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:28624600-28626600	Active TSS	Brain Anterior Caudate	brain
16	chr6:28624600-28627200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:28624600-28627200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr6:28624800-28625000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:28624800-28625000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28624800-28625000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
21	chr6:28624800-28625000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28624800-28625000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
23	chr6:28624800-28625000	Enhancers	A549	lung
24	chr6:28624800-28625200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28624800-28625200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:28624800-28625200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
27	chr6:28624800-28625200	Enhancers	Placenta	Placenta
28	chr6:28624800-28625400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:28624800-28625400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr6:28624800-28625400	Bivalent/Poised TSS	GM12878-XiMat	blood
31	chr6:28624800-28625600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr6:28624800-28625600	Bivalent/Poised TSS	Fetal Kidney	kidney
33	chr6:28624800-28626000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:28624800-28626800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:28624800-28626800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:28624800-28626800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:28624800-28626800	Active TSS	Ovary	ovary
38	chr6:28624800-28626800	Active TSS	Hela-S3	cervix
39	chr6:28624800-28627000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:28624800-28627000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr6:28624800-28627000	Active TSS	Brain Angular Gyrus	brain
42	chr6:28624800-28627000	Active TSS	Brain Cingulate Gyrus	brain
43	chr6:28624800-28627000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:28624800-28627200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:28624800-28627200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:28624800-28627200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:28624800-28627200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28624800-28627200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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