Variant report

Variant	rs61240102
Chromosome Location	chr6:27124904-27124905
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27124529..27127097-chr6:27791591..27794445,2	K562	blood:
2	chr6:27122310..27125099-chr6:27797389..27799861,3	K562	blood:
3	chr6:27124582..27127541-chr6:27758021..27760797,2	K562	blood:
4	chr6:27123211..27127154-chr6:27858700..27862425,3	K562	blood:
5	chr6:27124529..27126942-chr6:27720154..27721836,2	K562	blood:
6	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
7	chr6:26155627..26158355-chr6:27123950..27127373,3	K562	blood:
8	chr6:27124141..27131442-chr6:27773840..27780959,15	K562	blood:
9	chr17:41465610..41467876-chr6:27123814..27125644,2	MCF-7	breast:
10	chr6:27124780..27127221-chr6:27160550..27163070,2	K562	blood:
11	chr6:27124389..27126074-chr6:27173688..27175728,2	K562	blood:
12	chr6:26986606..26988221-chr6:27124102..27125749,2	K562	blood:
13	chr6:27124335..27127582-chr6:27143975..27147070,5	MCF-7	breast:
14	chr6:27124460..27128154-chr6:27128397..27131899,6	MCF-7	breast:
15	chr6:26239620..26242431-chr6:27124638..27127382,2	MCF-7	breast:
16	chr6:27094500..27095526-chr6:27124814..27125750,5	MCF-7	breast:
17	chr6:26102621..26104943-chr6:27124339..27126497,2	K562	blood:
18	chr6:27124395..27126679-chr6:27463309..27464874,2	K562	blood:
19	chr6:27122310..27124979-chr6:27798185..27799861,2	K562	blood:
20	chr6:27123092..27125641-chr6:27774464..27776969,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197914	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000238621	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000182611	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13194053	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219181	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34569203	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34783558	0.92[AMR][1000 genomes]
rs67330695	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67540232	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904071	1.00[ASN][1000 genomes]
rs6913660	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914824	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934329	0.95[AMR][1000 genomes]
rs72842197	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926300	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61240102	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs61240102	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs61240102	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27115600-27125000	Weak transcription	Right Atrium	heart
2	chr6:27122200-27125000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:27122200-27125000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:27123200-27125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:27123400-27125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:27123400-27125000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:27123400-27125000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:27123400-27125000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:27123400-27125000	Weak transcription	Fetal Thymus	thymus
10	chr6:27123400-27125200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:27123400-27125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:27123600-27125000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:27123600-27125200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:27124000-27125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:27124200-27125000	Active TSS	GM12878-XiMat	blood
16	chr6:27124200-27125200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:27124200-27125200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:27124600-27125000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:27124600-27126000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:27124800-27125000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:27124800-27125000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:27124800-27125000	Enhancers	Primary B cells from cord blood	blood
23	chr6:27124800-27125000	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:27124800-27125000	Active TSS	Primary T cells from cord blood	blood
25	chr6:27124800-27125000	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:27124800-27125000	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:27124800-27125000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:27124800-27125000	Enhancers	Adipose Nuclei	Adipose
29	chr6:27124800-27125000	Enhancers	Liver	Liver
30	chr6:27124800-27125000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr6:27124800-27125000	Flanking Active TSS	Fetal Lung	lung
32	chr6:27124800-27125000	Enhancers	Placenta	Placenta
33	chr6:27124800-27125000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr6:27124800-27125000	Flanking Active TSS	Thymus	Thymus
35	chr6:27124800-27125000	Flanking Active TSS	Hela-S3	cervix
36	chr6:27124800-27125000	Active TSS	HMEC	breast
37	chr6:27124800-27125200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:27124800-27125200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:27124800-27125200	Active TSS	Duodenum Mucosa	Duodenum
40	chr6:27124800-27125200	Flanking Active TSS	K562	blood
41	chr6:27124800-27125200	Active TSS	Osteobl	bone
42	chr6:27124800-27125400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:27124800-27125400	Active TSS	Fetal Intestine Small	intestine
44	chr6:27124800-27125600	Active TSS	NHEK	skin
45	chr6:27124800-27125800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr6:27124800-27125800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:27124800-27125800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:27124800-27126000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:27124800-27126000	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr6:27124800-27126000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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