Variant report

Variant	rs10516146
Chromosome Location	chr5:179166974-179166975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179166037..179167644-chr5:179247104..179249289,2	MCF-7	breast:
2	chr5:179124936..179127262-chr5:179166759..179169638,2	MCF-7	breast:
3	chr5:179048884..179051841-chr5:179165484..179167251,2	MCF-7	breast:
4	chr5:179165749..179167250-chr5:179170923..179173814,2	K562	blood:
5	chr5:179165284..179168030-chr5:179172314..179174869,3	K562	blood:
6	chr5:179158325..179161845-chr5:179164655..179167335,4	K562	blood:
7	chr5:179049878..179051432-chr5:179164385..179167213,2	K562	blood:
8	chr5:179166206..179168517-chr5:179176476..179179040,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000127022	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1019443	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs10447303	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10447304	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10794700	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10903245	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12374446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12374485	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522926	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs13172893	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13174472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13182141	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs13184690	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34329357	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34646062	0.85[CEU][hapmap]
rs34785307	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35320050	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3797774	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56227602	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56807514	0.91[EUR][1000 genomes]
rs62404348	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406180	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601073	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7736300	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10516146	CANX	cis	cerebellum	SCAN
rs10516146	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs10516146	CANX	cis	multi-tissue	Pritchard
rs10516146	CANX	cis	parietal	SCAN
rs10516146	MAML1	cis	lymphoblastoid	seeQTL
rs10516146	C5orf45	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161000-179174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179161000-179174000	Weak transcription	Gastric	stomach
3	chr5:179161000-179174200	Weak transcription	Esophagus	oesophagus
4	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
5	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179161600-179176600	Weak transcription	HSMMtube	muscle
8	chr5:179161800-179174200	Weak transcription	A549	lung
9	chr5:179161800-179176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:179161800-179176800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
12	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
13	chr5:179162000-179168200	Weak transcription	Psoas Muscle	Psoas
14	chr5:179162000-179168600	Strong transcription	Fetal Stomach	stomach
15	chr5:179162000-179174000	Weak transcription	Liver	Liver
16	chr5:179162000-179176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:179162000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:179162000-179176600	Weak transcription	Osteobl	bone
19	chr5:179162000-179176800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:179162000-179181200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:179162000-179181400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:179162000-179181800	Weak transcription	NHLF	lung
23	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:179162000-179186000	Weak transcription	HSMM	muscle
25	chr5:179162000-179186200	Weak transcription	HMEC	breast
26	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
27	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:179162800-179168600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:179163000-179176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:179163200-179167000	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:179163200-179176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:179163200-179176800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:179163200-179181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:179163400-179167600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:179163400-179168200	Strong transcription	Fetal Thymus	thymus
37	chr5:179163400-179168800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:179163400-179173800	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:179163400-179174000	Weak transcription	Right Atrium	heart
40	chr5:179163400-179174000	Weak transcription	Right Ventricle	heart
41	chr5:179163400-179175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:179163400-179176600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:179163600-179167000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:179163600-179174000	Weak transcription	Small Intestine	intestine
45	chr5:179163800-179167000	Weak transcription	Lung	lung
46	chr5:179163800-179180000	Weak transcription	Fetal Brain Male	brain
47	chr5:179164000-179167000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr5:179164000-179168400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:179164200-179167000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr5:179164200-179167200	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links