Variant report

Variant	rs10516298
Chromosome Location	chr4:16164230-16164231
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:
2	chr4:16152453..16154569-chr4:16162351..16164254,2	K562	blood:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10034719	0.81[ASN][1000 genomes]
rs10516299	0.90[CHD][hapmap]
rs10939653	0.97[CHD][hapmap];0.87[JPT][hapmap]
rs11724076	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11724423	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724467	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11731602	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736424	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736827	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12504884	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12506478	0.90[ASN][1000 genomes]
rs12513244	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12643544	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12645055	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12651110	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1373112	0.92[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1662652	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662654	0.85[CHD][hapmap]
rs16893099	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16893119	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16893138	0.89[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16893143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16893144	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16893147	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16893158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178450	0.87[CHD][hapmap]
rs317869	0.85[CHD][hapmap]
rs317874	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs317878	0.87[CHD][hapmap]
rs35851218	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56023844	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56218994	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57089965	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58047733	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60460559	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60768295	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73128422	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73128457	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130433	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73130439	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73130445	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73130449	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73130451	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73130453	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73130456	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs894639	0.90[CHD][hapmap];0.93[JPT][hapmap]

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
rs10516298	MYO6	trans	lymphoblastoid	seeQTL
rs10516298	IL1R1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 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	chr4:16153000-16164400	Weak transcription	NH-A	brain
3	chr4:16153200-16165200	Weak transcription	HSMM	muscle
4	chr4:16153600-16165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:16154800-16164400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:16157000-16164400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr4:16157200-16166800	Weak transcription	Brain Angular Gyrus	brain
8	chr4:16157600-16164600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:16157800-16164400	Weak transcription	Brain Anterior Caudate	brain
10	chr4:16157800-16164600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:16157800-16170600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:16157800-16180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:16157800-16180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:16158000-16165000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:16158000-16175400	Weak transcription	NHDF-Ad	bronchial
16	chr4:16158200-16164400	Weak transcription	Fetal Stomach	stomach
17	chr4:16159400-16164600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:16159600-16164800	Weak transcription	K562	blood
19	chr4:16159800-16167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:16160000-16164600	Weak transcription	Brain Germinal Matrix	brain
21	chr4:16160000-16167600	Weak transcription	HepG2	liver
22	chr4:16160200-16164400	Weak transcription	Fetal Brain Female	brain
23	chr4:16160200-16164600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:16160200-16164600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:16160200-16164800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:16160200-16165000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:16160200-16173800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:16160400-16164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:16160400-16164600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:16160400-16164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:16160400-16165000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:16160400-16165000	Weak transcription	Right Ventricle	heart
33	chr4:16160400-16165200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:16160400-16166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:16160400-16167800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:16160400-16182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:16160600-16164400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:16160600-16164400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:16160600-16167800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:16160600-16172200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:16160800-16176800	Strong transcription	Primary B cells from cord blood	blood
42	chr4:16161000-16182600	Strong transcription	Fetal Thymus	thymus
43	chr4:16161400-16164400	Weak transcription	GM12878-XiMat	blood
44	chr4:16161600-16176200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:16161600-16181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:16161600-16182600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr4:16161600-16182800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:16161600-16186000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:16161800-16164600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:16161800-16170000	Strong transcription	Adipose Nuclei	Adipose

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