Variant report

Variant	rs36012762
Chromosome Location	chr6:25980523-25980524
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25967844..25969475-chr6:25980365..25983085,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1045537	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10484433	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10484435	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13191776	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13192365	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13192713	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13193424	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13195279	0.84[EUR][1000 genomes]
rs13195692	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13196552	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13197334	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13200797	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13200888	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13201821	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13202371	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13203673	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13206443	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13206501	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13207673	0.84[EUR][1000 genomes]
rs13210399	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13212652	0.83[EUR][1000 genomes]
rs13214280	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13216785	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220395	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13220488	0.84[EUR][1000 genomes]
rs16891235	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16891261	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16891264	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16891315	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16891334	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17586553	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17586784	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17587226	0.81[EUR][1000 genomes]
rs17587597	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2051539	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28360595	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34027471	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34116162	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34233736	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34391493	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs34791189	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34804024	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35069699	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35116528	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35169013	0.84[EUR][1000 genomes]
rs35249036	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35335639	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35367169	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35378061	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35402046	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35484309	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35528636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35778245	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35825164	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35902160	0.91[ASN][1000 genomes]
rs3734528	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3752417	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56195001	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56294283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60512607	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66790453	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67296946	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67491322	0.81[EUR][1000 genomes]
rs67844427	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68149500	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71557315	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71557316	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72832596	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72834617	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72834623	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7749414	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	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
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
9	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs36012762	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs36012762	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25964400-25981400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:25965600-25985600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:25967200-25981000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:25967200-25992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:25967800-25992000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:25968400-25981200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:25968400-25985600	Strong transcription	Primary hematopoietic stem cells	blood
8	chr6:25968400-25987600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:25968600-25986000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr6:25968600-25987200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr6:25968800-25986600	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr6:25968800-25989400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr6:25969000-25986600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:25969000-25989600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:25969200-25989400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:25971400-25987200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:25971400-25989400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:25972200-25986000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:25972200-25987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:25972200-25988600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:25972400-25980600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:25972400-25985400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:25972400-25986200	Strong transcription	NHDF-Ad	bronchial
24	chr6:25972400-25986600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:25972400-25987200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:25972400-25987400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:25972400-25988800	Strong transcription	HSMM	muscle
28	chr6:25972600-25985800	Strong transcription	HUVEC	blood vessel
29	chr6:25972600-25986200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:25972600-25986600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr6:25972600-25988600	Strong transcription	Osteobl	bone
32	chr6:25972800-25986400	Strong transcription	Liver	Liver
33	chr6:25972800-25992000	Weak transcription	Right Ventricle	heart
34	chr6:25973000-25980600	Weak transcription	Pancreas	Pancrea
35	chr6:25973000-25986000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:25973600-25981200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:25973600-25987000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:25973600-25988000	Strong transcription	Placenta	Placenta
39	chr6:25973600-25989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25974600-25981200	Weak transcription	Fetal Kidney	kidney
41	chr6:25974600-25987600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:25974800-25981400	Weak transcription	K562	blood
43	chr6:25974800-25983400	Weak transcription	Psoas Muscle	Psoas
44	chr6:25974800-25992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:25974800-25992000	Weak transcription	A549	lung
46	chr6:25975200-25982200	Weak transcription	Stomach Mucosa	stomach
47	chr6:25975200-25987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:25975200-25988600	Strong transcription	Primary B cells from cord blood	blood
49	chr6:25975400-25981400	Weak transcription	Hela-S3	cervix
50	chr6:25975600-25982400	Weak transcription	HMEC	breast

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