Variant report

Variant	rs9986596
Chromosome Location	chr6:28219661-28219662
allele	A/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	chr6:28218740..28220554-chr6:28234465..28236739,2	MCF-7	breast:
2	chr6:28109464..28110985-chr6:28218502..28221254,2	MCF-7	breast:
3	chr6:28129539..28132293-chr6:28218155..28220468,2	K562	blood:
4	chr6:28192051..28194433-chr6:28219534..28221191,2	MCF-7	breast:
5	chr6:28105046..28106642-chr6:28218504..28220928,2	K562	blood:
6	chr6:28103203..28105926-chr6:28219159..28220709,2	MCF-7	breast:
7	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
8	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
9	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
10	chr6:28217257..28219975-chr6:28319678..28321725,2	K562	blood:
11	chr6:28109506..28111867-chr6:28218476..28220389,2	K562	blood:
12	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
13	chr6:28185564..28187470-chr6:28218621..28220714,2	MCF-7	breast:
14	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
15	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
16	chr6:28104411..28106188-chr6:28216933..28220029,3	MCF-7	breast:
17	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
18	chr6:28217084..28219662-chr6:28271676..28274035,2	K562	blood:
19	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:
20	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226314	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10456362	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076639	0.81[ASN][1000 genomes]
rs11755032	0.90[ASN][1000 genomes]
rs11965538	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13200462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339899	0.88[ASN][1000 genomes]
rs1419183	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679709	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679732	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778507	0.93[ASN][1000 genomes]
rs1778508	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778511	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936365	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2743554	0.96[ASN][1000 genomes]
rs2743555	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799077	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799079	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61127718	0.80[ASN][1000 genomes]
rs68141011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905391	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920512	0.91[ASN][1000 genomes]
rs735765	0.91[EUR][1000 genomes]
rs7740487	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853676	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853678	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853679	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853681	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853682	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853685	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853687	0.81[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366717	0.80[EUR][1000 genomes]
rs9393908	0.80[EUR][1000 genomes]
rs9461446	0.93[ASN][1000 genomes]
rs9461448	0.90[ASN][1000 genomes]
rs9461449	0.90[ASN][1000 genomes]
rs9468321	0.93[ASN][1000 genomes]
rs9468322	0.93[ASN][1000 genomes]
rs9468342	0.81[ASN][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9986596	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9986596	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs9986596	AL022393.7	cis	Muscle Skeletal	GTEx
rs9986596	RP5-874C20.3	cis	Thyroid	GTEx
rs9986596	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9986596	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28218200-28220200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:28218400-28220200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:28218400-28220200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:28218400-28220200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:28218400-28220400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:28218400-28220400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:28218400-28220600	Active TSS	A549	lung
8	chr6:28218600-28220200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:28218600-28220200	Active TSS	HSMMtube	muscle
10	chr6:28218600-28220800	Flanking Active TSS	Liver	Liver
11	chr6:28218800-28220200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:28218800-28220200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:28218800-28220200	Active TSS	Colonic Mucosa	Colon
14	chr6:28218800-28220200	Active TSS	Fetal Intestine Large	intestine
15	chr6:28218800-28220200	Active TSS	Right Atrium	heart
16	chr6:28218800-28220400	Active TSS	Ovary	ovary
17	chr6:28218800-28220400	Active TSS	Psoas Muscle	Psoas
18	chr6:28218800-28220400	Active TSS	Right Ventricle	heart
19	chr6:28218800-28220400	Active TSS	GM12878-XiMat	blood
20	chr6:28218800-28220400	Active TSS	HSMM	muscle
21	chr6:28219000-28220000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:28219000-28220000	Active TSS	Brain Cingulate Gyrus	brain
23	chr6:28219000-28220000	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr6:28219000-28220000	Active TSS	K562	blood
25	chr6:28219000-28220200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:28219000-28220200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:28219000-28220200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28219000-28220200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:28219000-28220200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:28219000-28220200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:28219000-28220200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:28219000-28220200	Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:28219000-28220200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:28219000-28220200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28219000-28220200	Active TSS	Brain Angular Gyrus	brain
36	chr6:28219000-28220200	Active TSS	Brain Hippocampus Middle	brain
37	chr6:28219000-28220200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:28219000-28220200	Active TSS	Colon Smooth Muscle	Colon
39	chr6:28219000-28220200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:28219000-28220200	Active TSS	Fetal Brain Male	brain
41	chr6:28219000-28220200	Active TSS	Fetal Brain Female	brain
42	chr6:28219000-28220200	Active TSS	Fetal Heart	heart
43	chr6:28219000-28220200	Active TSS	Fetal Intestine Small	intestine
44	chr6:28219000-28220200	Active TSS	Fetal Lung	lung
45	chr6:28219000-28220200	Active TSS	Fetal Muscle Trunk	muscle
46	chr6:28219000-28220200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:28219000-28220200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:28219000-28220200	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr6:28219000-28220200	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:28219000-28220200	Active TSS	Hela-S3	cervix

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