Variant report

Variant	rs3800318
Chromosome Location	chr6:27263641-27263642
allele	A/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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27261653..27264204-chr6:27341617..27343820,2	K562	blood:
2	chr6:27261806..27264755-chr6:27859413..27861745,2	K562	blood:
3	chr6:27260766..27263711-chr6:27659606..27661608,2	K562	blood:
4	chr6:27263089..27265493-chr6:27438139..27440840,3	MCF-7	breast:
5	chr6:27097893..27101461-chr6:27263240..27264846,3	K562	blood:
6	chr6:27219267..27221635-chr6:27262171..27265020,3	K562	blood:
7	chr6:27180877..27182881-chr6:27262753..27266056,3	K562	blood:
8	chr6:27218297..27220785-chr6:27262344..27265020,2	K562	blood:
9	chr6:27263474..27265071-chr6:27275388..27277708,2	K562	blood:
10	chr6:27263338..27266126-chr6:27718637..27721483,2	K562	blood:
11	chr6:27255029..27257456-chr6:27262507..27264289,2	MCF-7	breast:
12	chr6:27254367..27256212-chr6:27263059..27265882,2	MCF-7	breast:
13	chr6:27116381..27118425-chr6:27261911..27264171,2	K562	blood:
14	chr6:27197041..27202373-chr6:27261458..27267425,7	K562	blood:
15	chr6:27261110..27263869-chr6:27440100..27444366,4	K562	blood:
16	chr6:27262330..27264270-chr6:27461597..27464387,2	K562	blood:
17	chr6:27246057..27248417-chr6:27262936..27265446,2	MCF-7	breast:
18	chr6:27262603..27264877-chr6:27278498..27281369,2	K562	blood:
19	chr6:27261602..27264204-chr6:27341617..27343393,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000158553	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11755662	1.00[JPT][hapmap]
rs12664426	1.00[JPT][hapmap]
rs13211166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897282	1.00[CHB][hapmap]
rs16897515	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2893910	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800316	1.00[JPT][hapmap]
rs6921711	1.00[JPT][hapmap]
rs6938200	1.00[JPT][hapmap]
rs72839449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746199	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760931	1.00[JPT][hapmap]

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	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
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800318	BTN3A2	cis	Whole Blood	GTEx
rs3800318	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs3800318	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs3800318	BTN3A2	cis	Muscle Skeletal	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27261000-27263800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:27261000-27264600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:27261000-27264600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr6:27261000-27265600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:27261000-27266400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:27261000-27266400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:27261000-27266800	Active TSS	A549	lung
8	chr6:27261400-27266400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:27261400-27266400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:27261400-27266400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:27261600-27264600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:27262200-27263800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:27262200-27264000	Flanking Active TSS	K562	blood
14	chr6:27262200-27264000	Flanking Active TSS	NHEK	skin
15	chr6:27262200-27264200	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr6:27262600-27266400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:27262800-27264000	Flanking Active TSS	Hela-S3	cervix
18	chr6:27262800-27264000	Flanking Active TSS	HMEC	breast
19	chr6:27262800-27266000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:27263000-27264200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr6:27263000-27266400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr6:27263200-27264200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:27263200-27264800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:27263200-27264800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:27263200-27265400	Active TSS	HSMMtube	muscle
26	chr6:27263200-27265800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:27263200-27266000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:27263400-27263800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
29	chr6:27263400-27263800	Flanking Bivalent TSS/Enh	Placenta	Placenta
30	chr6:27263400-27264200	Active TSS	NH-A	brain
31	chr6:27263400-27264400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
32	chr6:27263400-27264600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:27263400-27264600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr6:27263400-27264600	Bivalent/Poised TSS	NHDF-Ad	bronchial
35	chr6:27263400-27264800	Flanking Active TSS	Osteobl	bone
36	chr6:27263400-27265000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
37	chr6:27263400-27265200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:27263400-27265800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:27263400-27265800	Active TSS	NHLF	lung
40	chr6:27263400-27266200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:27263400-27266200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:27263400-27266200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:27263600-27263800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:27263600-27263800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:27263600-27263800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
46	chr6:27263600-27263800	Bivalent Enhancer	Fetal Kidney	kidney
47	chr6:27263600-27263800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
48	chr6:27263600-27264000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
49	chr6:27263600-27264000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:27263600-27264000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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