Variant report

Variant	rs9478192
Chromosome Location	chr6:150183737-150183738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:150181876-150186422	IMR90	lung:	n/a	n/a
2	MAFF	chr6:150183473-150183749	K562	blood:	n/a	chr6:150183650-150183668
3	CHD1	chr6:150181747-150185902	IMR90	lung:	n/a	chr6:150185305-150185315
4	MAFK	chr6:150183466-150183814	HepG2	liver:	n/a	chr6:150183651-150183666
5	MAFK	chr6:150182648-150183826	IMR90	lung:	n/a	chr6:150183213-150183224 chr6:150183651-150183666
6	MAFF	chr6:150183496-150183768	HepG2	liver:	n/a	chr6:150183650-150183668
7	POLR2A	chr6:150181811-150186475	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr6:150180156-150183754	HepG2	liver:	n/a	n/a
9	MAFK	chr6:150183488-150183796	HepG2	liver:	n/a	chr6:150183651-150183666

No.	Distal block	Cell Line	Cell type
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150037075..150038991-chr6:150181496..150184249,2	K562	blood:
3	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:
4	chr6:150036146..150038991-chr6:150182749..150185016,3	K562	blood:

Variant related genes	Relation type
ENSG00000268592	TF binding region
ENSG00000164520	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000203722	Chromatin interaction
ENSG00000223701	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1334510	0.83[EUR][1000 genomes]
rs2095376	0.86[EUR][1000 genomes]
rs2342767	0.81[EUR][1000 genomes]
rs2342769	0.81[EUR][1000 genomes]
rs2342770	0.81[EUR][1000 genomes]
rs3823021	0.81[EUR][1000 genomes]
rs4869763	0.81[EUR][1000 genomes]
rs4869764	0.81[EUR][1000 genomes]
rs6557133	0.84[EUR][1000 genomes]
rs6933882	0.81[EUR][1000 genomes]
rs6935829	0.80[EUR][1000 genomes]
rs6939761	0.81[EUR][1000 genomes]
rs7740145	0.81[EUR][1000 genomes]
rs7742692	0.81[EUR][1000 genomes]
rs7742993	0.81[EUR][1000 genomes]
rs7744821	0.81[EUR][1000 genomes]
rs7747457	0.81[EUR][1000 genomes]
rs7753544	0.81[EUR][1000 genomes]
rs7756850	0.80[EUR][1000 genomes]
rs7757972	0.81[EUR][1000 genomes]
rs7758020	0.81[EUR][1000 genomes]
rs7758033	0.81[EUR][1000 genomes]
rs7763719	0.82[EUR][1000 genomes]
rs7763849	0.81[EUR][1000 genomes]
rs7764376	0.81[EUR][1000 genomes]
rs7767588	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7767592	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7768626	0.81[EUR][1000 genomes]
rs7768665	0.81[EUR][1000 genomes]
rs7769118	0.80[EUR][1000 genomes]
rs7774787	0.81[EUR][1000 genomes]
rs9322225	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9322228	0.81[EUR][1000 genomes]
rs9371215	0.84[EUR][1000 genomes]
rs9371504	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371505	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371542	0.80[AMR][1000 genomes]
rs9371544	0.81[EUR][1000 genomes]
rs9383577	0.80[EUR][1000 genomes]
rs9383584	0.81[EUR][1000 genomes]
rs9383912	0.81[EUR][1000 genomes]
rs9383913	0.81[EUR][1000 genomes]
rs9383914	0.81[EUR][1000 genomes]
rs9383921	0.80[EUR][1000 genomes]
rs9397058	0.81[EUR][1000 genomes]
rs9397398	0.84[EUR][1000 genomes]
rs9397420	0.81[EUR][1000 genomes]
rs9397434	0.81[EUR][1000 genomes]
rs9968871	0.80[EUR][1000 genomes]
rs9969044	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3437961	chr6:150182459-150187257	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv823860	chr6:150183482-150186226	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9478192	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9478192	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9478192	NUP43	cis	Whole Blood	GTEx
rs9478192	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9478192	RAET1G	cis	Skin Sun Exposed Lower leg	GTEx
rs9478192	RP11-350J20.9	cis	Muscle Skeletal	GTEx
rs9478192	RAET1G	cis	Artery Tibial	GTEx
rs9478192	RP11-350J20.9	cis	lung	GTEx
rs9478192	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9478192	RP11-350J20.5	cis	Thyroid	GTEx
rs9478192	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9478192	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9478192	RP11-350J20.5	cis	lung	GTEx
rs9478192	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9478192	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9478192	RAET1G	cis	Thyroid	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150173000-150184200	Weak transcription	Aorta	Aorta
2	chr6:150178600-150184000	Weak transcription	Psoas Muscle	Psoas
3	chr6:150180600-150184200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:150181200-150183800	Enhancers	Fetal Muscle Leg	muscle
5	chr6:150181200-150183800	Enhancers	Placenta	Placenta
6	chr6:150181200-150183800	Enhancers	Pancreas	Pancrea
7	chr6:150181200-150183800	Flanking Active TSS	Hela-S3	cervix
8	chr6:150181200-150184000	Enhancers	Liver	Liver
9	chr6:150181800-150183800	Enhancers	Adipose Nuclei	Adipose
10	chr6:150181800-150183800	Enhancers	Brain Germinal Matrix	brain
11	chr6:150182000-150184000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr6:150182000-150184000	Enhancers	Left Ventricle	heart
13	chr6:150182000-150184000	Enhancers	Stomach Mucosa	stomach
14	chr6:150182000-150186200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:150182200-150184200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:150182200-150184200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:150182400-150183800	Flanking Active TSS	Osteobl	bone
18	chr6:150182400-150184200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:150182600-150183800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:150182600-150183800	Enhancers	Fetal Muscle Trunk	muscle
21	chr6:150182600-150184000	Enhancers	Dnd41	blood
22	chr6:150182800-150183800	Flanking Active TSS	HepG2	liver
23	chr6:150183000-150183800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:150183000-150184000	Enhancers	Brain Substantia Nigra	brain
25	chr6:150183000-150184000	Enhancers	Fetal Brain Male	brain
26	chr6:150183000-150184000	Enhancers	Fetal Kidney	kidney
27	chr6:150183200-150183800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr6:150183200-150183800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:150183200-150183800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:150183200-150183800	Enhancers	Colonic Mucosa	Colon
31	chr6:150183200-150183800	Enhancers	Ovary	ovary
32	chr6:150183200-150183800	Enhancers	Right Atrium	heart
33	chr6:150183200-150183800	Flanking Active TSS	NHDF-Ad	bronchial
34	chr6:150183200-150184000	Enhancers	Fetal Heart	heart
35	chr6:150183200-150184000	Enhancers	Fetal Intestine Large	intestine
36	chr6:150183200-150184000	Enhancers	Fetal Intestine Small	intestine
37	chr6:150183200-150184000	Enhancers	Fetal Lung	lung
38	chr6:150183200-150184000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:150183200-150184200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:150183400-150183800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:150183400-150183800	Flanking Active TSS	Fetal Brain Female	brain
42	chr6:150183400-150183800	Weak transcription	Right Ventricle	heart
43	chr6:150183400-150183800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr6:150183400-150183800	Flanking Active TSS	HMEC	breast
45	chr6:150183400-150183800	Flanking Active TSS	NHEK	skin
46	chr6:150183400-150184000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr6:150183400-150184000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:150183400-150184000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:150183400-150184000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:150183400-150184000	Enhancers	Brain Hippocampus Middle	brain

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