Variant report

Variant	rs3799379
Chromosome Location	chr6:26404694-26404695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26403709..26405372-chr6:26410974..26412511,2	MCF-7	breast:
2	chr6:26402676..26405446-chr6:26406042..26411352,6	K562	blood:
3	chr6:26403327..26405922-chr6:26411445..26413266,2	K562	blood:
4	chr6:26400774..26405587-chr6:26406042..26409897,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTN2A2-1	chr6:26404363-26404783	NONHSAT108276

Variant related genes	Relation type
ENSG00000026950	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10946813	0.81[CEU][hapmap]
rs12214031	0.81[CEU][hapmap]
rs12663780	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1624440	0.84[JPT][hapmap]
rs2072804	0.83[ASN][1000 genomes]
rs2076029	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237236	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3208733	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3846845	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846846	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4320356	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4712984	0.88[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs4712987	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712998	0.82[CHB][hapmap]
rs6907924	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7356988	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366657	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379860	0.81[CEU][hapmap]
rs9379874	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467722	0.81[CEU][hapmap]
rs9467736	0.81[ASN][1000 genomes]
rs9467737	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv883491	chr6:26367689-26410800	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv883492	chr6:26367689-26436592	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv883493	chr6:26367689-26442786	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv883494	chr6:26367833-26442786	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv883495	chr6:26367833-26443853	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3334611	chr6:26367893-26443308	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	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
13	nsv883496	chr6:26369549-26413088	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv883497	chr6:26369549-26442786	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv883498	chr6:26369549-26443853	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1030863	chr6:26371006-26405990	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
18	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799379	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26394000-26412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26401800-26404800	Weak transcription	Spleen	Spleen
3	chr6:26402800-26404800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:26402800-26405200	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr6:26402800-26405200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:26402800-26405200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:26403000-26405200	Weak transcription	Esophagus	oesophagus
8	chr6:26403000-26405200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:26403000-26406400	Weak transcription	Gastric	stomach
10	chr6:26403000-26406800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:26403000-26406800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:26403000-26409600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:26403000-26409600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:26403000-26409800	Weak transcription	Aorta	Aorta
15	chr6:26403000-26410000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:26403000-26421200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:26403000-26421200	Weak transcription	Right Ventricle	heart
18	chr6:26403200-26405000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr6:26403200-26405000	Enhancers	Ovary	ovary
20	chr6:26403200-26405200	Enhancers	Fetal Thymus	thymus
21	chr6:26403200-26405600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:26403200-26406800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:26403200-26406800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:26403200-26407200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:26403200-26408000	Weak transcription	HUVEC	blood vessel
26	chr6:26403200-26409400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:26403200-26409400	Weak transcription	Fetal Heart	heart
28	chr6:26403200-26409600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:26403200-26412200	Weak transcription	Brain Angular Gyrus	brain
30	chr6:26403200-26415400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:26403200-26415600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:26403200-26420200	Weak transcription	HSMMtube	muscle
33	chr6:26403200-26421000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:26403200-26421000	Weak transcription	NHDF-Ad	bronchial
35	chr6:26403400-26404800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr6:26403400-26404800	Enhancers	Colon Smooth Muscle	Colon
37	chr6:26403400-26405200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:26403400-26405200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr6:26403400-26405400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:26403400-26405400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:26403400-26405400	Enhancers	HepG2	liver
42	chr6:26403400-26405600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:26403400-26405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:26403400-26406600	Weak transcription	Brain Anterior Caudate	brain
45	chr6:26403400-26406800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:26403400-26406800	Weak transcription	Placenta	Placenta
47	chr6:26403400-26407000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:26403400-26407200	Weak transcription	Brain Substantia Nigra	brain
49	chr6:26403400-26407400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:26403400-26407400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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