Variant report

Variant	rs34396849
Chromosome Location	chr6:28250955-28250956
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
2	chr6:28180671..28183155-chr6:28250254..28252159,2	K562	blood:
3	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
4	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
5	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
6	chr6:28232995..28235984-chr6:28248211..28251032,3	MCF-7	breast:
7	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
8	chr6:28249727..28254264-chr6:28300327..28304071,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs13190888	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13191786	1.00[EUR][1000 genomes]
rs13195291	0.93[EUR][1000 genomes]
rs13197574	0.85[EUR][1000 genomes]
rs13197633	0.93[EUR][1000 genomes]
rs13198809	0.93[EUR][1000 genomes]
rs13201308	0.85[EUR][1000 genomes]
rs13201681	0.93[EUR][1000 genomes]
rs13203816	0.85[EUR][1000 genomes]
rs13204012	1.00[EUR][1000 genomes]
rs13205211	1.00[EUR][1000 genomes]
rs13205911	0.85[EUR][1000 genomes]
rs13207345	1.00[EUR][1000 genomes]
rs13208096	1.00[EUR][1000 genomes]
rs13211507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213152	0.93[EUR][1000 genomes]
rs13213986	0.89[EUR][1000 genomes]
rs13214023	0.93[EUR][1000 genomes]
rs13217619	0.93[EUR][1000 genomes]
rs13217984	0.85[EUR][1000 genomes]
rs2232423	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232426	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232429	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33932084	0.98[EUR][1000 genomes]
rs34166054	0.85[EUR][1000 genomes]
rs34218844	1.00[EUR][1000 genomes]
rs34243448	1.00[EUR][1000 genomes]
rs34371502	0.85[EUR][1000 genomes]
rs34505829	0.85[EUR][1000 genomes]
rs34546986	0.89[EUR][1000 genomes]
rs34588114	0.85[EUR][1000 genomes]
rs34661125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34676049	0.93[EUR][1000 genomes]
rs34691223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34765154	0.85[EUR][1000 genomes]
rs34832585	0.85[EUR][1000 genomes]
rs34871267	0.89[EUR][1000 genomes]
rs34878803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34950484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35001169	0.93[EUR][1000 genomes]
rs35016036	0.96[EUR][1000 genomes]
rs35017208	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35030260	0.98[EUR][1000 genomes]
rs35072899	1.00[EUR][1000 genomes]
rs35098436	0.85[EUR][1000 genomes]
rs35345226	0.85[EUR][1000 genomes]
rs35353359	0.93[EUR][1000 genomes]
rs35656932	0.93[EUR][1000 genomes]
rs35744819	0.93[EUR][1000 genomes]
rs35749575	0.85[EUR][1000 genomes]
rs35781323	0.85[EUR][1000 genomes]
rs35883476	0.89[EUR][1000 genomes]
rs35902873	0.85[EUR][1000 genomes]
rs36092177	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55690788	0.93[EUR][1000 genomes]
rs56075693	1.00[EUR][1000 genomes]
rs56189111	1.00[EUR][1000 genomes]
rs66886492	0.85[EUR][1000 genomes]
rs67297533	0.82[EUR][1000 genomes]
rs67340775	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67381177	0.93[EUR][1000 genomes]
rs67981811	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67998226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559070	0.85[EUR][1000 genomes]
rs71559072	0.85[EUR][1000 genomes]
rs72846780	0.85[EUR][1000 genomes]
rs72846794	0.85[EUR][1000 genomes]
rs72854513	1.00[EUR][1000 genomes]
rs7752608	0.81[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34396849	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs34396849	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34396849	AL022393.7	cis	Muscle Skeletal	GTEx
rs34396849	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28248200-28251000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:28248800-28251000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:28249000-28251000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28249000-28251000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28249000-28251000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:28249000-28251000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:28249000-28251000	Active TSS	HSMM	muscle
8	chr6:28249200-28251200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:28249800-28251000	Flanking Active TSS	Dnd41	blood
10	chr6:28249800-28251600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
12	chr6:28250000-28251000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:28250000-28251600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:28250000-28251600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:28250000-28251600	Weak transcription	Aorta	Aorta
16	chr6:28250000-28251600	Weak transcription	Lung	lung
17	chr6:28250000-28251800	Weak transcription	Ovary	ovary
18	chr6:28250000-28252200	Weak transcription	Fetal Intestine Large	intestine
19	chr6:28250000-28253200	Weak transcription	Placenta	Placenta
20	chr6:28250000-28254800	Weak transcription	Primary B cells from cord blood	blood
21	chr6:28250000-28254800	Weak transcription	Pancreas	Pancrea
22	chr6:28250000-28254800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28250000-28255000	Weak transcription	Esophagus	oesophagus
24	chr6:28250000-28258000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:28250000-28258600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:28250000-28293800	Weak transcription	Gastric	stomach
28	chr6:28250200-28251000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:28250200-28251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:28250200-28251000	Weak transcription	Brain Substantia Nigra	brain
31	chr6:28250200-28251000	Enhancers	Left Ventricle	heart
32	chr6:28250200-28251600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:28250200-28251600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:28250200-28251600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28250200-28251600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:28250200-28251600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:28250200-28251600	Weak transcription	Fetal Stomach	stomach
38	chr6:28250200-28251800	Weak transcription	Brain Angular Gyrus	brain
39	chr6:28250200-28252800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
41	chr6:28250400-28251000	Weak transcription	Osteobl	bone
42	chr6:28250400-28251200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:28250400-28251200	Active TSS	Colon Smooth Muscle	Colon
44	chr6:28250400-28251200	Enhancers	HepG2	liver
45	chr6:28250400-28251400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr6:28250400-28251400	ZNF genes & repeats	K562	blood
47	chr6:28250400-28251600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:28250400-28251600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:28250400-28251600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:28250400-28252200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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