Variant report

Variant	rs4688021
Chromosome Location	chr3:119363566-119363567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:119363445-119363619	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119361516..119364108-chr3:119364269..119367239,2	K562	blood:

Variant related genes	Relation type
POPDC2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11914676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12487499	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12492456	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525836	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203235	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2670292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688629	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2688634	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692616	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35256565	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484809	0.85[JPT][hapmap]
rs524043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571352	0.85[JPT][hapmap]
rs572119	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766563	0.89[CHB][hapmap]
rs67683909	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.95[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	0.88[JPT][hapmap]
rs6803814	0.89[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7626940	0.89[CHB][hapmap]
rs8422	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4688021	COX17	Cis_1M	lymphoblastoid	RTeQTL
rs4688021	POPDC2	cis	lymphoblastoid	seeQTL
rs4688021	POPDC2	cis	multi-tissue	Pritchard
rs4688021	COX17	cis	lymphoblastoid	seeQTL
rs4688021	RP11-190C22.1	cis	Heart Left Ventricle	GTEx
rs4688021	ILDR1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119341400-119364600	Weak transcription	Liver	Liver
2	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
4	chr3:119352600-119367000	Weak transcription	Ovary	ovary
5	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:119356800-119364800	Weak transcription	Stomach Mucosa	stomach
8	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
12	chr3:119357800-119366600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:119357800-119367000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
18	chr3:119358200-119366200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:119358400-119366800	Weak transcription	Esophagus	oesophagus
21	chr3:119358400-119367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:119358600-119365200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:119358600-119366600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:119359800-119363600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr3:119360400-119366600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:119360600-119363800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:119360600-119365400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:119360800-119367800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:119361000-119363600	Weak transcription	Fetal Brain Male	brain
34	chr3:119361000-119363600	Enhancers	NHDF-Ad	bronchial
35	chr3:119361000-119363800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:119361000-119363800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:119361200-119363600	Enhancers	HSMM	muscle
38	chr3:119361200-119365800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:119361200-119366800	Weak transcription	Pancreas	Pancrea
40	chr3:119361200-119367000	Weak transcription	Gastric	stomach
41	chr3:119361200-119369000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
43	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
44	chr3:119361400-119363600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:119361400-119363600	Enhancers	Osteobl	bone
46	chr3:119361400-119366200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:119361400-119366200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:119361400-119366800	Weak transcription	Spleen	Spleen
49	chr3:119361400-119372600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain

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