Variant report

Variant	rs2297846
Chromosome Location	chr6:145148111-145148112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10499237	0.85[YRI][hapmap]
rs11546879	0.88[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs13195905	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13198393	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13202460	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13204600	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13208243	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs13208561	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13210728	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13212915	0.81[AMR][1000 genomes]
rs13213382	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13218938	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1856418	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2297844	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2297845	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35415004	0.81[AMR][1000 genomes]
rs36083145	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131501	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4143180	0.94[ASN][1000 genomes]
rs4476850	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4495289	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4631314	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4642498	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9321993	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9373428	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373431	0.88[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9376855	0.81[EUR][1000 genomes]
rs9376858	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9386082	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386084	0.96[ASN][1000 genomes]
rs9390219	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9390240	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9399506	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399508	0.83[EUR][1000 genomes]
rs9399509	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9399513	0.81[AMR][1000 genomes]
rs9403603	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403610	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403616	0.90[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[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
rs2297846	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:103 , 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	chr6:145116000-145148600	Weak transcription	Placenta	Placenta
6	chr6:145116000-145154800	Weak transcription	Spleen	Spleen
7	chr6:145116000-145155800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:145116200-145154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:145116400-145155600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:145116400-145169000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:145117400-145175200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:145117600-145148400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:145119200-145155800	Weak transcription	Pancreas	Pancrea
14	chr6:145120000-145148800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:145120000-145155000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:145120200-145148400	Weak transcription	Ovary	ovary
17	chr6:145120200-145156400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:145120600-145148200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:145120600-145148400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:145120600-145148800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:145120600-145154800	Weak transcription	Aorta	Aorta
22	chr6:145120800-145148400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:145120800-145155800	Weak transcription	Thymus	Thymus
24	chr6:145126000-145148200	Weak transcription	HUVEC	blood vessel
25	chr6:145126600-145169400	Weak transcription	Stomach Mucosa	stomach
26	chr6:145127000-145148600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:145127600-145148400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:145130600-145163800	Weak transcription	NHEK	skin
29	chr6:145130800-145156800	Weak transcription	Osteobl	bone
30	chr6:145130800-145172200	Weak transcription	NH-A	brain
31	chr6:145131000-145148600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:145131000-145156600	Weak transcription	NHLF	lung
33	chr6:145131000-145157000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:145132800-145155600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:145135200-145149000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:145135400-145148200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:145135400-145148200	Weak transcription	Fetal Intestine Large	intestine
38	chr6:145135400-145152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:145135400-145166000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:145135600-145155800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:145135600-145156800	Weak transcription	Lung	lung
42	chr6:145135600-145157600	Weak transcription	GM12878-XiMat	blood
43	chr6:145137000-145148400	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:145137400-145148200	Weak transcription	Liver	Liver
45	chr6:145137400-145148200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:145137400-145157000	Weak transcription	Psoas Muscle	Psoas
47	chr6:145137400-145176800	Weak transcription	Fetal Heart	heart
48	chr6:145137800-145175800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:145138000-145155000	Weak transcription	Colonic Mucosa	Colon
50	chr6:145139600-145150200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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