Variant report

Variant	rs9468350
Chromosome Location	chr6:28319107-28319108
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: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	chr6:28247642..28250446-chr6:28317779..28319288,2	K562	blood:
2	chr6:28225627..28229530-chr6:28318492..28321477,3	K562	blood:
3	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
4	chr6:28247366..28250224-chr6:28317764..28319401,2	MCF-7	breast:
5	chr6:28318312..28320612-chr6:28351068..28352730,2	K562	blood:
6	chr6:28228030..28230750-chr6:28318492..28321168,2	K562	blood:
7	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
8	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
9	chr6:28192912..28194626-chr6:28318304..28321178,2	MCF-7	breast:
10	chr6:27636377..27638707-chr6:28318162..28320333,2	K562	blood:
11	chr6:28318727..28321441-chr6:28336675..28338219,2	K562	blood:
12	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
13	chr6:28182735..28195387-chr6:28315960..28325841,32	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	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
18	chr6:28317772..28319708-chr6:28509467..28511768,2	K562	blood:
19	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1119211	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11970439	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13210258	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17301128	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2799081	0.81[EUR][1000 genomes]
rs56131013	0.95[EUR][1000 genomes]
rs6456814	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6456816	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903652	0.95[EUR][1000 genomes]
rs6903823	0.94[EUR][1000 genomes]
rs6912584	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6921919	0.86[EUR][1000 genomes]
rs6922111	0.86[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9468350	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9468350	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9468350	RP5-874C20.3	cis	Thyroid	GTEx
rs9468350	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468350	ZSCAN23	cis	Artery Tibial	GTEx
rs9468350	ZSCAN23	cis	Muscle Skeletal	GTEx
rs9468350	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317200-28319200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28317200-28319200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:28317200-28319400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:28317200-28319400	Active TSS	Right Atrium	heart
5	chr6:28317200-28319600	Active TSS	HSMM	muscle
6	chr6:28317200-28322000	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:28317200-28322200	Active TSS	Stomach Smooth Muscle	stomach
8	chr6:28318000-28319200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:28318000-28319200	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr6:28318000-28319400	Flanking Active TSS	Liver	Liver
11	chr6:28318000-28319400	Flanking Active TSS	Dnd41	blood
12	chr6:28318000-28319600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:28318200-28319200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:28318200-28319200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:28318200-28319200	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr6:28318200-28319200	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr6:28318200-28319200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr6:28318200-28319200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr6:28318200-28319200	Flanking Active TSS	HMEC	breast
20	chr6:28318200-28319200	Flanking Active TSS	NHEK	skin
21	chr6:28318200-28319400	Flanking Active TSS	HUVEC	blood vessel
22	chr6:28318200-28319600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:28318200-28321800	Weak transcription	Spleen	Spleen
24	chr6:28318200-28322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:28318400-28319200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:28318400-28319200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28318400-28319200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr6:28318400-28319200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:28318400-28319200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:28318400-28319200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:28318400-28319200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:28318400-28319200	Flanking Active TSS	Fetal Brain Female	brain
33	chr6:28318400-28319200	Flanking Active TSS	Fetal Heart	heart
34	chr6:28318400-28319200	Enhancers	Fetal Thymus	thymus
35	chr6:28318400-28319200	Enhancers	Left Ventricle	heart
36	chr6:28318400-28319200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:28318400-28319200	Enhancers	Right Ventricle	heart
38	chr6:28318400-28319400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:28318400-28319400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:28318400-28319400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:28318400-28319400	Enhancers	Pancreas	Pancrea
42	chr6:28318400-28320800	Weak transcription	Esophagus	oesophagus
43	chr6:28318400-28321600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:28318400-28321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:28318400-28321800	Weak transcription	Gastric	stomach
46	chr6:28318400-28322200	Weak transcription	Placenta	Placenta
47	chr6:28318400-28323000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links