Variant report

Variant	rs6456739
Chromosome Location	chr6:26604140-26604141
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26602899..26604701-chr6:27090642..27092939,2	MCF-7	breast:
2	chr6:26345126..26347534-chr6:26601972..26604774,2	K562	blood:
3	chr6:26253763..26255321-chr6:26603498..26605821,2	K562	blood:
4	chr6:26602910..26606507-chr6:26613473..26615906,4	K562	blood:
5	chr6:26601646..26604594-chr6:26657057..26659318,2	K562	blood:
6	chr6:26603453..26605542-chr6:26624989..26626923,2	K562	blood:
7	chr6:26549776..26551317-chr6:26603406..26604964,2	K562	blood:
8	chr6:26583725..26585701-chr6:26603112..26605724,2	K562	blood:
9	chr6:26603782..26606678-chr6:27060300..27062978,2	K562	blood:
10	chr6:26603403..26605480-chr6:27094143..27096233,2	K562	blood:
11	chr6:26603268..26605367-chr6:27170113..27172922,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272468	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2451715	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2451716	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2451739	0.86[ASN][1000 genomes]
rs2451746	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2451752	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2451753	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2494691	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2494705	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2494711	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2498342	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3800302	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs3800303	0.81[AMR][1000 genomes]
rs3807029	0.93[ASN][1000 genomes]
rs4368798	0.81[AMR][1000 genomes]
rs4591839	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs6911540	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6915555	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs6919391	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs6925087	0.81[AMR][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs7767847	0.81[AMR][1000 genomes]
rs9379892	0.84[JPT][hapmap]
rs9379902	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs9379903	0.91[ASN][1000 genomes]
rs9461275	0.82[AMR][1000 genomes]
rs9461276	0.81[AMR][1000 genomes]
rs9467810	0.83[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6456739	BTN3A3	cis	cerebellum	SCAN
rs6456739	ZNF322	cis	Artery Tibial	GTEx
rs6456739	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6456739	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs6456739	BTN3A2	cis	cerebellum	SCAN
rs6456739	RP11-457M11.2	cis	Artery Tibial	GTEx
rs6456739	HIST1H4L	cis	parietal	SCAN
rs6456739	ZNF204P	cis	cerebellum	SCAN
rs6456739	RP11-457M11.2	cis	lung	GTEx
rs6456739	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs6456739	BTN2A2	cis	cerebellum	SCAN
rs6456739	BTN3A2	cis	parietal	SCAN
rs6456739	BTN3A1	cis	cerebellum	SCAN
rs6456739	HIST1H3F	cis	cerebellum	SCAN
rs6456739	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs6456739	ZNF322	cis	Nerve Tibial	GTEx
rs6456739	RP11-457M11.2	cis	Thyroid	GTEx
rs6456739	ZNF322	cis	Thyroid	GTEx
rs6456739	HIST1H3E	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26598000-26604800	Weak transcription	Aorta	Aorta
2	chr6:26598000-26606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:26598200-26607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:26599200-26607800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:26599200-26607800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:26599200-26607800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:26599400-26607800	Weak transcription	Fetal Intestine Small	intestine
8	chr6:26599600-26607800	Weak transcription	Colonic Mucosa	Colon
9	chr6:26599800-26607800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:26600000-26604400	Weak transcription	HUVEC	blood vessel
11	chr6:26600000-26607800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:26600000-26607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:26600000-26607800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:26600000-26607800	Weak transcription	Fetal Stomach	stomach
15	chr6:26600000-26607800	Weak transcription	Thymus	Thymus
16	chr6:26600000-26607800	Weak transcription	HepG2	liver
17	chr6:26600000-26607800	Weak transcription	NHLF	lung
18	chr6:26600000-26614000	Weak transcription	Spleen	Spleen
19	chr6:26600200-26604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:26600200-26607200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:26600200-26607600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:26600200-26607600	Weak transcription	Hela-S3	cervix
23	chr6:26600200-26607800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr6:26600200-26607800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:26600200-26607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:26600200-26607800	Weak transcription	Fetal Kidney	kidney
27	chr6:26600200-26607800	Weak transcription	Dnd41	blood
28	chr6:26600200-26607800	Weak transcription	HMEC	breast
29	chr6:26600200-26607800	Weak transcription	Osteobl	bone
30	chr6:26600400-26607800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:26600400-26607800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:26600400-26607800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:26600400-26607800	Weak transcription	Liver	Liver
34	chr6:26600400-26607800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:26600400-26607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:26600400-26607800	Weak transcription	Ovary	ovary
37	chr6:26600400-26607800	Weak transcription	A549	lung
38	chr6:26600400-26607800	Weak transcription	NHDF-Ad	bronchial
39	chr6:26600600-26605800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:26600600-26607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:26600600-26607800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:26600600-26607800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:26600600-26607800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:26600600-26607800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:26600600-26607800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:26600600-26607800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:26600800-26605000	Weak transcription	K562	blood
48	chr6:26600800-26607000	Weak transcription	Fetal Brain Female	brain
49	chr6:26600800-26607600	Weak transcription	Brain Anterior Caudate	brain
50	chr6:26600800-26607600	Weak transcription	Brain Inferior Temporal Lobe	brain

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