Variant report

Variant	rs57252182
Chromosome Location	chr6:27720249-27720250
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27218569..27220460-chr6:27719318..27721940,3	MCF-7	breast:
2	chr6:27598278..27599262-chr6:27720193..27721073,2	K562	blood:
3	chr6:27516133..27518259-chr6:27720231..27723733,3	K562	blood:
4	chr6:27144211..27146855-chr6:27719701..27721733,2	K562	blood:
5	chr6:27635070..27638218-chr6:27719785..27722837,4	K562	blood:
6	chr6:27615823..27619826-chr6:27718831..27721663,4	K562	blood:
7	chr6:27654225..27656931-chr6:27719778..27721751,2	K562	blood:
8	chr6:27129261..27130116-chr6:27719696..27720311,2	MCF-7	breast:
9	chr6:27615823..27619826-chr6:27719510..27721663,4	K562	blood:
10	chr6:27716568..27718796-chr6:27718856..27720931,2	K562	blood:
11	chr6:27263338..27266126-chr6:27718637..27721483,2	K562	blood:
12	chr6:27713445..27716447-chr6:27717145..27720805,5	K562	blood:
13	chr6:27558583..27561214-chr6:27719565..27721812,2	K562	blood:
14	chr6:27704721..27706812-chr6:27718654..27720926,2	K562	blood:
15	chr6:27113190..27116258-chr6:27719531..27723256,5	K562	blood:
16	chr6:27486493..27487200-chr6:27719731..27720643,4	K562	blood:
17	chr6:27686786..27690624-chr6:27717358..27721129,5	K562	blood:
18	chr6:27719685..27721542-chr6:27859391..27861101,2	MCF-7	breast:
19	chr6:27113421..27116397-chr6:27720119..27723593,4	K562	blood:
20	chr6:27520849..27522507-chr6:27719657..27722145,3	K562	blood:
21	chr6:27661606..27663243-chr6:27719625..27721150,2	K562	blood:
22	chr6:27652463..27655224-chr6:27720018..27721922,3	K562	blood:
23	chr6:27124529..27126942-chr6:27720154..27721836,2	K562	blood:
24	chr6:27510934..27513659-chr6:27719612..27722020,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction
ENSG00000238648	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000216915	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs200480	0.80[ASN][1000 genomes]
rs2056924	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2179096	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713120	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295747	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348772	0.83[EUR][1000 genomes]
rs9366699	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9368527	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9380007	0.86[EUR][1000 genomes]
rs9468209	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468213	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57252182	AL022393.7	cis	Muscle Skeletal	GTEx
rs57252182	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27719800-27722200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:27719800-27722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr6:27719800-27722400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:27720000-27720400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:27720000-27721400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:27720000-27722000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:27720000-27722000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:27720000-27722000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:27720000-27722200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:27720000-27722200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:27720000-27722200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:27720000-27722200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27720000-27722200	Active TSS	Brain Hippocampus Middle	brain
14	chr6:27720000-27722200	Active TSS	Thymus	Thymus
15	chr6:27720000-27722400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:27720000-27722400	Active TSS	Brain Anterior Caudate	brain
17	chr6:27720000-27722400	Active TSS	Brain Germinal Matrix	brain
18	chr6:27720000-27722600	Active TSS	Fetal Kidney	kidney
19	chr6:27720000-27723000	Active TSS	A549	lung
20	chr6:27720200-27720400	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr6:27720200-27720400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr6:27720200-27720400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr6:27720200-27720400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr6:27720200-27720400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr6:27720200-27720400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:27720200-27720400	Flanking Active TSS	Liver	Liver
27	chr6:27720200-27720600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr6:27720200-27720600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:27720200-27720600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr6:27720200-27720600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:27720200-27720600	Flanking Active TSS	Fetal Thymus	thymus
32	chr6:27720200-27721000	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr6:27720200-27721000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:27720200-27721200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:27720200-27721200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:27720200-27721200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:27720200-27721200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:27720200-27721200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:27720200-27721200	Active TSS	Esophagus	oesophagus
40	chr6:27720200-27721200	Active TSS	Fetal Heart	heart
41	chr6:27720200-27721200	Active TSS	Lung	lung
42	chr6:27720200-27721200	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr6:27720200-27721200	Active TSS	Small Intestine	intestine
44	chr6:27720200-27721200	Active TSS	Stomach Mucosa	stomach
45	chr6:27720200-27721400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr6:27720200-27721400	Active TSS	Primary T cells from cord blood	blood
47	chr6:27720200-27721800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:27720200-27721800	Active TSS	Primary monocytes fromperipheralblood	blood
49	chr6:27720200-27721800	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:27720200-27721800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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