Variant report

Variant	rs2456928
Chromosome Location	chr4:48156135-48156136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10016563	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10021919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033663	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1159075	1.00[JPT][hapmap]
rs11942525	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs16861044	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16861106	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs16861108	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17470919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471024	1.00[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs17471142	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs17574399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661532	0.84[ASN][1000 genomes]
rs2661535	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28408546	0.87[ASN][1000 genomes]
rs28538414	0.87[ASN][1000 genomes]
rs28702422	0.96[EUR][1000 genomes]
rs3749503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792619	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55683170	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55809586	0.88[EUR][1000 genomes]
rs6814046	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6814614	0.89[EUR][1000 genomes]
rs6819804	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829390	0.88[JPT][hapmap]
rs6837324	0.86[GIH][hapmap]
rs73244489	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654182	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682890	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684558	0.91[EUR][1000 genomes]
rs955692	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991974	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2456928	TEC	cis	parietal	SCAN
rs2456928	TXK	cis	parietal	SCAN
rs2456928	FRYL	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
3	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
5	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:48138400-48157400	Weak transcription	Aorta	Aorta
8	chr4:48139200-48157600	Weak transcription	Gastric	stomach
9	chr4:48139200-48159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:48140200-48157400	Weak transcription	Pancreas	Pancrea
11	chr4:48143000-48157600	Weak transcription	Fetal Thymus	thymus
12	chr4:48143000-48157600	Weak transcription	Thymus	Thymus
13	chr4:48144800-48157200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:48150000-48164000	Weak transcription	Hela-S3	cervix
15	chr4:48152400-48157200	Weak transcription	Fetal Heart	heart
16	chr4:48152600-48156800	Weak transcription	Liver	Liver
17	chr4:48152600-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:48152600-48157200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:48152600-48163200	Weak transcription	HSMMtube	muscle
20	chr4:48152600-48164000	Weak transcription	HSMM	muscle
21	chr4:48153000-48160400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:48155200-48158800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr4:48155200-48159400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:48155400-48158600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr4:48155400-48159600	ZNF genes & repeats	GM12878-XiMat	blood
26	chr4:48155400-48160000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:48155600-48156200	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr4:48155600-48156200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:48155600-48156200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
30	chr4:48155600-48156400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:48155600-48156400	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr4:48155600-48158400	ZNF genes & repeats	Psoas Muscle	Psoas
33	chr4:48155800-48156200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
34	chr4:48155800-48156400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:48155800-48158400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
36	chr4:48155800-48158400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
37	chr4:48155800-48158400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr4:48155800-48158400	ZNF genes & repeats	K562	blood
39	chr4:48155800-48158800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr4:48155800-48158800	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr4:48155800-48158800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:48155800-48159400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:48156000-48156800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:48156000-48157400	Weak transcription	Left Ventricle	heart
45	chr4:48156000-48157600	Weak transcription	Lung	lung
46	chr4:48156000-48157600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:48156000-48159600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr4:48156000-48168000	Weak transcription	Esophagus	oesophagus

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