Variant report

Variant	rs35744819
Chromosome Location	chr6:28318331-28318332
allele	G/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28247642..28250446-chr6:28317779..28319288,2	K562	blood:
2	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
3	chr6:28247366..28250224-chr6:28317764..28319401,2	MCF-7	breast:
4	chr6:28318312..28320612-chr6:28351068..28352730,2	K562	blood:
5	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
6	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
7	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
8	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
9	chr6:28192912..28194626-chr6:28318304..28321178,2	MCF-7	breast:
10	chr6:27636377..27638707-chr6:28318162..28320333,2	K562	blood:
11	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
12	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
13	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:
14	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
15	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
16	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
17	chr6:28317772..28319708-chr6:28509467..28511768,2	K562	blood:
18	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs13190888	0.88[EUR][1000 genomes]
rs13191038	0.93[EUR][1000 genomes]
rs13191786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13195291	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13197633	0.93[EUR][1000 genomes]
rs13198809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13201308	0.85[EUR][1000 genomes]
rs13201681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203816	0.85[EUR][1000 genomes]
rs13204012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205211	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205911	0.85[EUR][1000 genomes]
rs13207345	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13208096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13211507	0.93[EUR][1000 genomes]
rs13213152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213986	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13214023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217619	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217984	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2232423	0.96[EUR][1000 genomes]
rs2232426	0.96[EUR][1000 genomes]
rs2232429	0.96[EUR][1000 genomes]
rs33932084	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34218844	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34243448	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34371502	0.85[EUR][1000 genomes]
rs34396849	0.93[EUR][1000 genomes]
rs34505829	0.85[EUR][1000 genomes]
rs34546986	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34588114	0.85[EUR][1000 genomes]
rs34661125	0.93[EUR][1000 genomes]
rs34676049	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34691223	0.93[EUR][1000 genomes]
rs34765154	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34832585	0.85[EUR][1000 genomes]
rs34871267	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34878803	0.93[EUR][1000 genomes]
rs34950484	0.93[EUR][1000 genomes]
rs35001169	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35016036	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35017208	1.00[EUR][1000 genomes]
rs35030260	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35072899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35098436	0.85[EUR][1000 genomes]
rs35345226	0.85[EUR][1000 genomes]
rs35353359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35656932	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35749575	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35781323	0.85[EUR][1000 genomes]
rs35883476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36092177	0.96[EUR][1000 genomes]
rs55690788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56075693	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56189111	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66886492	0.85[EUR][1000 genomes]
rs67297533	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67340775	0.94[EUR][1000 genomes]
rs67381177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67981811	0.96[EUR][1000 genomes]
rs67998226	0.93[EUR][1000 genomes]
rs71559072	0.85[EUR][1000 genomes]
rs72846780	0.85[EUR][1000 genomes]
rs72846794	0.85[EUR][1000 genomes]
rs72854513	1.00[AMR][1000 genomes];0.93[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
rs35744819	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35744819	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs35744819	AL022393.7	cis	Muscle Skeletal	GTEx
rs35744819	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317000-28318400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:28317000-28318400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:28317000-28318400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:28317000-28318400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:28317000-28318800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:28317000-28319000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:28317000-28319000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28317200-28318400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:28317200-28318400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:28317200-28318400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28317200-28318400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:28317200-28318400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr6:28317200-28318400	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:28317200-28318400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:28317200-28318400	Active TSS	Aorta	Aorta
16	chr6:28317200-28318400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:28317200-28318400	Active TSS	Fetal Heart	heart
18	chr6:28317200-28318400	Active TSS	Fetal Intestine Large	intestine
19	chr6:28317200-28318400	Active TSS	Fetal Kidney	kidney
20	chr6:28317200-28318400	Active TSS	Fetal Muscle Trunk	muscle
21	chr6:28317200-28318400	Active TSS	Placenta	Placenta
22	chr6:28317200-28318400	Active TSS	Left Ventricle	heart
23	chr6:28317200-28318400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:28317200-28318400	Active TSS	A549	lung
25	chr6:28317200-28318400	Bivalent/Poised TSS	HepG2	liver
26	chr6:28317200-28318600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:28317200-28318600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:28317200-28318600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:28317200-28318600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:28317200-28318600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28317200-28318600	Active TSS	Brain Anterior Caudate	brain
32	chr6:28317200-28318600	Active TSS	Fetal Intestine Small	intestine
33	chr6:28317200-28318600	Active TSS	Placenta Amnion	Placenta Amnion
34	chr6:28317200-28318600	Active TSS	GM12878-XiMat	blood
35	chr6:28317200-28318600	Active TSS	NHDF-Ad	bronchial
36	chr6:28317200-28318800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr6:28317200-28318800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:28317200-28318800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:28317200-28318800	Active TSS	Brain Cingulate Gyrus	brain
40	chr6:28317200-28318800	Active TSS	Colonic Mucosa	Colon
41	chr6:28317200-28318800	Active TSS	Fetal Stomach	stomach
42	chr6:28317200-28318800	Active TSS	Ovary	ovary
43	chr6:28317200-28319000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr6:28317200-28319000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:28317200-28319000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:28317200-28319000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:28317200-28319000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:28317200-28319000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:28317200-28319000	Active TSS	HSMMtube	muscle
50	chr6:28317200-28319000	Active TSS	K562	blood

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