Variant report

Variant	rs10516297
Chromosome Location	chr4:16166404-16166405
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	chr4:16164227..16166422-chr4:16226469..16228031,2	K562	blood:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10017532	0.86[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs11730922	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110290	0.83[ASN][1000 genomes]
rs13120908	0.94[ASN][1000 genomes]
rs13132678	0.95[ASN][1000 genomes]
rs13136055	0.81[ASN][1000 genomes]
rs13136172	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs2028631	0.81[ASN][1000 genomes]
rs2872216	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33980476	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs34129131	0.89[ASN][1000 genomes]
rs34496855	0.90[ASN][1000 genomes]
rs34592687	0.90[ASN][1000 genomes]
rs34663238	0.90[ASN][1000 genomes]
rs35475888	0.94[ASN][1000 genomes]
rs35517826	0.93[ASN][1000 genomes]
rs35804424	0.90[ASN][1000 genomes]
rs35806798	0.93[ASN][1000 genomes]
rs35899968	0.90[ASN][1000 genomes]
rs3749544	0.86[ASN][1000 genomes]
rs4235382	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4698138	0.81[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs4698457	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs56353092	0.92[ASN][1000 genomes]
rs6810390	0.94[ASN][1000 genomes]
rs6823229	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6823230	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6852432	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10516297	LCORL	cis	cerebellum	SCAN
rs10516297	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16150800-16166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:16157200-16166800	Weak transcription	Brain Angular Gyrus	brain
3	chr4:16157800-16170600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:16157800-16180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:16157800-16180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:16158000-16175400	Weak transcription	NHDF-Ad	bronchial
7	chr4:16159800-16167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:16160000-16167600	Weak transcription	HepG2	liver
9	chr4:16160200-16173800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:16160400-16167800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:16160400-16182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:16160600-16167800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:16160600-16172200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:16160800-16176800	Strong transcription	Primary B cells from cord blood	blood
15	chr4:16161000-16182600	Strong transcription	Fetal Thymus	thymus
16	chr4:16161600-16176200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:16161600-16181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:16161600-16182600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:16161600-16182800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:16161600-16186000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:16161800-16170000	Strong transcription	Adipose Nuclei	Adipose
22	chr4:16161800-16193200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:16162000-16167200	Weak transcription	Osteobl	bone
24	chr4:16162000-16167400	Weak transcription	Psoas Muscle	Psoas
25	chr4:16162000-16175800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:16162200-16167800	Weak transcription	Fetal Brain Male	brain
27	chr4:16162200-16171200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:16162200-16182800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:16162400-16167200	Weak transcription	Fetal Kidney	kidney
30	chr4:16162400-16167600	Weak transcription	NHLF	lung
31	chr4:16162600-16166800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:16162600-16183200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:16163000-16171800	Strong transcription	Left Ventricle	heart
34	chr4:16163000-16172800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:16163000-16175600	Strong transcription	Primary T cells from cord blood	blood
36	chr4:16163000-16176400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:16163000-16182800	Strong transcription	Liver	Liver
38	chr4:16163000-16183200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:16163000-16183200	Strong transcription	Placenta	Placenta
40	chr4:16163200-16178200	Weak transcription	Fetal Heart	heart
41	chr4:16163200-16183400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:16163200-16183400	Weak transcription	Hela-S3	cervix
43	chr4:16163200-16195800	Weak transcription	HMEC	breast
44	chr4:16163400-16167600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:16163400-16168800	Strong transcription	Colon Smooth Muscle	Colon
46	chr4:16163400-16176000	Strong transcription	Dnd41	blood
47	chr4:16163600-16168400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr4:16163600-16168600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:16163600-16171800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:16163600-16172000	Strong transcription	Spleen	Spleen

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