Variant report

Variant	rs2297844
Chromosome Location	chr6:145148927-145148928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11546879	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13195905	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13198393	0.83[CHB][hapmap]
rs13202460	0.83[CHB][hapmap]
rs13204600	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13208243	0.86[CHB][hapmap];0.82[MEX][hapmap]
rs13208561	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13210728	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13212915	0.86[AMR][1000 genomes]
rs13213382	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13218938	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1856418	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2297845	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2297846	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs35415004	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs36083145	0.90[ASN][1000 genomes]
rs4131501	0.82[CHB][hapmap]
rs4143180	0.82[ASN][1000 genomes]
rs4476850	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4495289	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4631314	0.82[ASN][1000 genomes]
rs4642498	0.90[ASN][1000 genomes]
rs9321993	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9373428	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9373431	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9376858	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9386084	0.84[ASN][1000 genomes]
rs9390219	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9390240	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390242	0.82[AMR][1000 genomes]
rs9399506	0.84[ASN][1000 genomes]
rs9399508	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9399509	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9399513	0.86[AMR][1000 genomes]
rs9403603	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9403610	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9403616	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv886740	chr6:145105354-145199259	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv886741	chr6:145123326-145165362	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297844	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145084000-145155800	Weak transcription	Right Ventricle	heart
2	chr6:145099600-145165800	Weak transcription	Small Intestine	intestine
3	chr6:145115200-145155000	Weak transcription	Esophagus	oesophagus
4	chr6:145115800-145156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:145116000-145154800	Weak transcription	Spleen	Spleen
6	chr6:145116000-145155800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:145116200-145154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:145116400-145155600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:145116400-145169000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:145117400-145175200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:145119200-145155800	Weak transcription	Pancreas	Pancrea
12	chr6:145120000-145155000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:145120200-145156400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:145120600-145154800	Weak transcription	Aorta	Aorta
15	chr6:145120800-145155800	Weak transcription	Thymus	Thymus
16	chr6:145126600-145169400	Weak transcription	Stomach Mucosa	stomach
17	chr6:145130600-145163800	Weak transcription	NHEK	skin
18	chr6:145130800-145156800	Weak transcription	Osteobl	bone
19	chr6:145130800-145172200	Weak transcription	NH-A	brain
20	chr6:145131000-145156600	Weak transcription	NHLF	lung
21	chr6:145131000-145157000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:145132800-145155600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:145135200-145149000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:145135400-145152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:145135400-145166000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:145135600-145155800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:145135600-145156800	Weak transcription	Lung	lung
28	chr6:145135600-145157600	Weak transcription	GM12878-XiMat	blood
29	chr6:145137400-145157000	Weak transcription	Psoas Muscle	Psoas
30	chr6:145137400-145176800	Weak transcription	Fetal Heart	heart
31	chr6:145137800-145175800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr6:145138000-145155000	Weak transcription	Colonic Mucosa	Colon
33	chr6:145139600-145150200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:145140000-145155400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:145140200-145157000	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:145140200-145161600	Strong transcription	Primary B cells from cord blood	blood
37	chr6:145141400-145172000	Weak transcription	Brain Substantia Nigra	brain
38	chr6:145141400-145175200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:145142000-145171400	Weak transcription	HMEC	breast
40	chr6:145142200-145149600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:145142400-145155000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:145142400-145156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:145143000-145173600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:145144000-145150000	Strong transcription	Primary T cells from cord blood	blood
45	chr6:145144800-145150600	Strong transcription	Dnd41	blood
46	chr6:145144800-145150800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr6:145145200-145150800	Strong transcription	Fetal Thymus	thymus
48	chr6:145145200-145157200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:145145400-145149600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:145145400-145152200	Weak transcription	HSMMtube	muscle

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