Variant report

Variant	rs34246779
Chromosome Location	chr6:26549212-26549213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26547747..26549536-chr6:26553157..26556049,2	MCF-7	breast:
2	chr6:26360907..26362623-chr6:26548003..26549634,2	K562	blood:
3	chr6:26541650..26546578-chr6:26547247..26553909,5	MCF-7	breast:
4	chr6:26548933..26552351-chr6:26595010..26597972,3	MCF-7	breast:
5	chr6:26546606..26549431-chr6:26551498..26554971,7	K562	blood:
6	chr6:26548378..26550170-chr6:26555408..26557476,2	K562	blood:

Variant related genes	Relation type
ENSG00000146109	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13195509	0.89[EUR][1000 genomes]
rs13198716	0.91[AMR][1000 genomes]
rs13212985	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13220261	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34104395	0.89[EUR][1000 genomes]
rs34148261	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34605993	0.86[EUR][1000 genomes]
rs34781270	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35076545	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35277236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400317	0.91[AMR][1000 genomes]
rs35433030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35555795	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35627490	0.89[EUR][1000 genomes]
rs35680819	0.89[EUR][1000 genomes]
rs36033628	0.89[EUR][1000 genomes]
rs36162392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734542	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3734543	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3823158	0.89[EUR][1000 genomes]
rs45527431	0.91[AMR][1000 genomes]
rs66757203	0.89[EUR][1000 genomes]
rs66941101	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71557340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72843784	0.82[EUR][1000 genomes]
rs72844462	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845428	1.00[AFR][1000 genomes];1.00[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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34246779	BTN3A2	cis	Stomach	GTEx
rs34246779	BTN3A2	cis	Whole Blood	GTEx
rs34246779	BTN3A2	cis	Heart Left Ventricle	GTEx
rs34246779	BTN3A2	cis	Esophagus Mucosa	GTEx
rs34246779	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs34246779	BTN3A2	cis	Muscle Skeletal	GTEx
rs34246779	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs34246779	BTN3A2	cis	Artery Aorta	GTEx
rs34246779	BTN3A2	cis	Nerve Tibial	GTEx
rs34246779	BTN3A2	cis	lung	GTEx
rs34246779	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs34246779	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs34246779	BTN3A2	cis	Thyroid	GTEx
rs34246779	BTN3A2	cis	Artery Tibial	GTEx
rs34246779	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26539200-26550600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:26539400-26550600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:26539600-26549800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:26539600-26550400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:26539600-26550400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:26539600-26550400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:26539600-26550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:26539600-26553000	Weak transcription	Fetal Heart	heart
9	chr6:26539800-26550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:26539800-26550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:26539800-26550800	Weak transcription	Pancreas	Pancrea
12	chr6:26540000-26550800	Weak transcription	Lung	lung
13	chr6:26540200-26550000	Weak transcription	Fetal Kidney	kidney
14	chr6:26540200-26550400	Weak transcription	Colonic Mucosa	Colon
15	chr6:26540400-26550000	Weak transcription	Stomach Mucosa	stomach
16	chr6:26540400-26550400	Weak transcription	Brain Angular Gyrus	brain
17	chr6:26540400-26550400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:26540400-26550600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:26540600-26550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:26540600-26550000	Weak transcription	Small Intestine	intestine
21	chr6:26542000-26550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:26542200-26550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:26543200-26550400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:26545800-26550000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:26545800-26550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:26545800-26550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:26546000-26550200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:26546000-26550200	Weak transcription	HSMMtube	muscle
29	chr6:26546200-26550000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:26546200-26550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:26546200-26550000	Weak transcription	Fetal Stomach	stomach
32	chr6:26546200-26550200	Weak transcription	Brain Anterior Caudate	brain
33	chr6:26546200-26550200	Weak transcription	Fetal Intestine Small	intestine
34	chr6:26546200-26550200	Weak transcription	Thymus	Thymus
35	chr6:26546200-26550200	Weak transcription	HUVEC	blood vessel
36	chr6:26546200-26550400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:26546200-26550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:26546200-26550400	Weak transcription	Esophagus	oesophagus
39	chr6:26546200-26550400	Weak transcription	Left Ventricle	heart
40	chr6:26546200-26550400	Weak transcription	HepG2	liver
41	chr6:26546200-26550400	Weak transcription	NHDF-Ad	bronchial
42	chr6:26546200-26550600	Weak transcription	Aorta	Aorta
43	chr6:26546200-26550800	Weak transcription	Gastric	stomach
44	chr6:26546400-26550000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:26546400-26550200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:26546400-26550200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:26546400-26550200	Weak transcription	Primary T cells from cord blood	blood
48	chr6:26546400-26550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:26546400-26550200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:26546400-26550200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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