Variant report

Variant	rs34332556
Chromosome Location	chr6:27357414-27357415
allele	C/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27113785..27116304-chr6:27356399..27358052,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27114804..27117756-chr6:27356552..27360776,4	K562	blood:
4	chr6:27357105..27360959-chr6:27363374..27365305,4	K562	blood:
5	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
6	chr6:27341304..27343058-chr6:27356076..27357820,2	MCF-7	breast:
7	chr6:27342371..27343890-chr6:27355850..27358027,2	K562	blood:
8	chr6:27356907..27359078-chr6:27397692..27399728,2	K562	blood:
9	chr6:27291445..27294642-chr6:27355178..27358043,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000217862	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484399	0.81[EUR][1000 genomes]
rs13191227	0.96[EUR][1000 genomes]
rs13191474	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13195040	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13195636	0.83[EUR][1000 genomes]
rs13196692	0.96[EUR][1000 genomes]
rs13207689	0.98[EUR][1000 genomes]
rs13209332	0.83[EUR][1000 genomes]
rs13212562	0.80[EUR][1000 genomes]
rs13218537	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360634	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34071253	0.94[EUR][1000 genomes]
rs34196306	0.89[EUR][1000 genomes]
rs34573979	0.87[EUR][1000 genomes]
rs34613987	0.80[EUR][1000 genomes]
rs34864796	0.80[EUR][1000 genomes]
rs34953377	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34965299	0.83[EUR][1000 genomes]
rs35120058	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35716472	0.94[EUR][1000 genomes]
rs35848276	0.83[EUR][1000 genomes]
rs35984974	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269265	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56401801	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58616630	0.87[EUR][1000 genomes]
rs66785117	0.83[EUR][1000 genomes]
rs66841633	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67240003	0.80[EUR][1000 genomes]
rs67859638	0.98[EUR][1000 genomes]
rs6904596	0.80[EUR][1000 genomes]
rs71537559	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839477	0.94[EUR][1000 genomes]
rs7749305	0.80[EUR][1000 genomes]
rs9468033	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs34332556	BTN3A2	cis	Muscle Skeletal	GTEx
rs34332556	BTN3A2	cis	Artery Tibial	GTEx
rs34332556	BTN3A2	cis	Esophagus Muscularis	GTEx
rs34332556	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs34332556	BTN3A2	cis	Thyroid	GTEx
rs34332556	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs34332556	BTN3A2	cis	Esophagus Mucosa	GTEx
rs34332556	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs34332556	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34332556	BTN3A2	cis	Whole Blood	GTEx
rs34332556	BTN3A2	cis	Nerve Tibial	GTEx
rs34332556	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27355600-27357600	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:27355600-27358400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:27355800-27357600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27355800-27357600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:27355800-27357600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:27355800-27357600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27355800-27357600	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr6:27355800-27357600	Active TSS	Stomach Smooth Muscle	stomach
9	chr6:27355800-27357600	Active TSS	NHEK	skin
10	chr6:27355800-27357800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:27355800-27357800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27355800-27357800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:27355800-27357800	Active TSS	GM12878-XiMat	blood
14	chr6:27355800-27358000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:27355800-27358000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:27356000-27357600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:27356000-27357600	Active TSS	Fetal Stomach	stomach
18	chr6:27356000-27357600	Active TSS	Hela-S3	cervix
19	chr6:27356000-27357600	Active TSS	Osteobl	bone
20	chr6:27356000-27357800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:27356000-27357800	Active TSS	Primary B cells from cord blood	blood
22	chr6:27356200-27357600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:27356200-27357600	Active TSS	Brain Anterior Caudate	brain
24	chr6:27356200-27357800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:27356200-27357800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:27356200-27357800	Active TSS	Primary T cells from cord blood	blood
27	chr6:27356200-27358000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr6:27356400-27357600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:27356800-27357800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:27356800-27358000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:27357000-27357600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr6:27357000-27357600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
33	chr6:27357000-27357600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr6:27357000-27357600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr6:27357000-27357600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr6:27357000-27358000	Flanking Active TSS	Dnd41	blood
37	chr6:27357200-27357600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:27357200-27357600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr6:27357200-27357600	Enhancers	Gastric	stomach
40	chr6:27357200-27357800	Enhancers	Spleen	Spleen
41	chr6:27357200-27358200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:27357200-27362200	Weak transcription	Aorta	Aorta
43	chr6:27357200-27366600	Weak transcription	Left Ventricle	heart
44	chr6:27357400-27357600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:27357400-27357600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:27357400-27357600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:27357400-27357600	Active TSS	Primary hematopoietic stem cells	blood
48	chr6:27357400-27357600	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr6:27357400-27357600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr6:27357400-27357600	Active TSS	Brain Angular Gyrus	brain

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