Variant report

Variant	rs525916
Chromosome Location	chr3:119367782-119367783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119363598..119365543-chr3:119365969..119367975,2	MCF-7	breast:
2	chr3:119366599..119368508-chr3:119385647..119388287,2	MCF-7	breast:
3	chr3:119356916..119358623-chr3:119366628..119369264,2	K562	blood:
4	chr3:119367081..119370215-chr3:119370341..119373711,3	MCF-7	breast:
5	chr3:119367190..119369718-chr3:119370796..119372691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11914676	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12487499	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.94[ASN][1000 genomes]
rs12490779	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12492456	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525836	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203235	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2670292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688629	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688634	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692616	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35256565	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484809	0.85[JPT][hapmap]
rs524043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571352	0.85[JPT][hapmap]
rs572119	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766563	0.88[CHB][hapmap]
rs67683909	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790938	0.86[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6794579	0.83[JPT][hapmap]
rs6803814	0.87[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7626940	0.88[CHB][hapmap]
rs8422	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs525916	RP11-190C22.1	cis	Heart Left Ventricle	GTEx
rs525916	COX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
3	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
13	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:119360800-119367800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:119361200-119369000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
21	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:119361400-119372600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:119362200-119371400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:119362400-119368600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:119365000-119368000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:119365200-119372200	Enhancers	Right Atrium	heart
33	chr3:119365200-119387400	Weak transcription	Liver	Liver
34	chr3:119365400-119367800	Genic enhancers	Fetal Muscle Leg	muscle
35	chr3:119365400-119368800	Strong transcription	Primary T cells from cord blood	blood
36	chr3:119365400-119369000	Genic enhancers	Colon Smooth Muscle	Colon
37	chr3:119365600-119367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:119365600-119368000	Transcr. at gene 5' and 3'	Right Ventricle	heart
39	chr3:119365600-119368400	Enhancers	Psoas Muscle	Psoas
40	chr3:119366000-119368800	Weak transcription	HepG2	liver
41	chr3:119366200-119367800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:119366200-119368200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:119366600-119367800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:119367000-119367800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:119367000-119367800	Enhancers	Ovary	ovary
46	chr3:119367000-119371000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:119367000-119371000	Weak transcription	HSMM	muscle
48	chr3:119367200-119368400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:119367200-119368600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:119367200-119369400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links