Variant report

Variant	rs16844078
Chromosome Location	chr3:101297354-101297355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101296777..101299755-chr3:101301756..101303953,2	MCF-7	breast:
2	chr3:101296714..101298321-chr3:101395804..101398572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1078154	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556582	0.80[AMR][1000 genomes]
rs12629395	0.88[EUR][1000 genomes]
rs12631729	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062695	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13063994	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13065665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070567	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078121	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13097625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097712	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976944	1.00[ASN][1000 genomes]
rs34408425	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34774691	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34930373	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762735	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899303	0.82[AMR][1000 genomes]
rs6441619	0.89[EUR][1000 genomes]
rs6762367	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792847	0.89[EUR][1000 genomes]
rs71315243	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71315244	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71315245	0.88[EUR][1000 genomes]
rs71315246	0.89[EUR][1000 genomes]
rs7619122	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630598	0.89[EUR][1000 genomes]
rs7637805	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv965193	chr3:101294846-101297410	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16844078	RG9MTD1	cis	brain	BrainEAC
rs16844078	RG9MTD1	cis	temporal cortex	BrainEAC
rs16844078	RG9MTD1	cis	occipital cortex	BrainEAC
rs16844078	RG9MTD1	cis	hippocampus	BrainEAC
rs16844078	RG9MTD1	cis	inferior olivary nucleus	BrainEAC
rs16844078	RG9MTD1	cis	cerebellar cortex	BrainEAC
rs16844078	RG9MTD1	cis	frontal cortex	BrainEAC
rs16844078	RG9MTD1	cis	substantia nigra	BrainEAC
rs16844078	RG9MTD1	cis	intralobular white matter	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101294000-101298400	Weak transcription	Pancreas	Pancrea
2	chr3:101294000-101298400	Weak transcription	Small Intestine	intestine
3	chr3:101294000-101301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:101294000-101305200	Weak transcription	Esophagus	oesophagus
5	chr3:101294000-101312200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:101294200-101309000	Weak transcription	Colonic Mucosa	Colon
7	chr3:101294200-101310000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:101294200-101319400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:101294400-101298400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:101294400-101309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:101294600-101297600	Weak transcription	Fetal Lung	lung
12	chr3:101294600-101298600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:101294600-101298600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr3:101294800-101297400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:101294800-101297600	Weak transcription	HSMM	muscle
16	chr3:101294800-101298400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:101294800-101298400	Weak transcription	Right Ventricle	heart
18	chr3:101294800-101298600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:101294800-101301200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:101294800-101305200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:101295000-101297600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:101295000-101298400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:101295000-101298400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:101295000-101298400	Weak transcription	Liver	Liver
25	chr3:101295000-101298400	Weak transcription	Osteobl	bone
26	chr3:101295000-101298600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:101295000-101298600	Weak transcription	Fetal Kidney	kidney
28	chr3:101295000-101298600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:101295000-101298600	Genic enhancers	Dnd41	blood
30	chr3:101295000-101299600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:101295000-101300000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:101295000-101304000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:101295000-101304600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:101295000-101304600	Weak transcription	NHEK	skin
35	chr3:101295000-101305000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:101295000-101305000	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:101295000-101309400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:101295000-101310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:101295200-101298400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:101295200-101306800	Weak transcription	Psoas Muscle	Psoas
41	chr3:101295600-101297400	Genic enhancers	K562	blood
42	chr3:101295600-101297600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:101295600-101299000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:101295600-101299400	Strong transcription	Fetal Thymus	thymus
45	chr3:101295600-101300000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:101295600-101300200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:101295600-101300200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:101295600-101300400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:101295800-101305200	Weak transcription	Gastric	stomach
50	chr3:101295800-101315000	Weak transcription	Right Atrium	heart

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