Variant report

Variant	rs2024767
Chromosome Location	chr1:184705437-184705438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184703854..184706366-chr1:184709752..184714206,4	K562	blood:
2	chr1:184702362..184703932-chr1:184704085..184706758,2	K562	blood:
3	chr1:184705153..184707744-chr1:184942725..184944472,2	K562	blood:
4	chr1:184692283..184693990-chr1:184704527..184706346,2	K562	blood:

Variant related genes	Relation type
ENSG00000135842	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1040666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1046239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061508	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10752941	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797987	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911640	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911644	0.83[GIH][hapmap]
rs12032144	0.85[EUR][1000 genomes]
rs12043236	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12071631	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124714	0.86[EUR][1000 genomes]
rs12124929	0.87[GIH][hapmap]
rs12133674	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12567225	0.87[GIH][hapmap]
rs12567226	0.87[GIH][hapmap]
rs2024765	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2207733	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2333715	0.87[GIH][hapmap]
rs2333716	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35478695	0.85[EUR][1000 genomes]
rs3736757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3895196	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4469687	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4498770	0.81[EUR][1000 genomes]
rs4651230	0.85[GIH][hapmap]
rs6663178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6677073	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726427	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7523023	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7525074	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs861575	0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs861577	0.87[ASN][1000 genomes]
rs861578	0.91[GIH][hapmap]
rs861579	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs861581	0.91[GIH][hapmap]
rs861582	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9425339	0.81[ASN][1000 genomes]
rs9425341	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425343	0.87[GIH][hapmap]
rs9425633	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425634	0.82[EUR][1000 genomes]
rs9425635	0.83[EUR][1000 genomes]
rs9658937	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9661314	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs971080	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1010371	chr1:184663898-184709570	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1001244	chr1:184667198-184715195	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1849889	chr1:184667371-184718601	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv872584	chr1:184678290-184716457	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2024767	EDEM3	cis	Esophagus Muscularis	GTEx
rs2024767	PTRF	trans	cerebellum	SCAN
rs2024767	PRG4	cis	parietal	SCAN
rs2024767	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs2024767	EDEM3	cis	Nerve Tibial	GTEx
rs2024767	EDEM3	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184654000-184710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:184654200-184710000	Weak transcription	Esophagus	oesophagus
3	chr1:184658400-184706800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:184659200-184707000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:184661000-184705600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:184661200-184707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:184662200-184706600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:184665200-184706800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:184668400-184707000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr1:184669200-184707000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:184669400-184707000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:184671200-184707400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:184674600-184723000	Weak transcription	Aorta	Aorta
14	chr1:184677600-184723200	Weak transcription	Lung	lung
15	chr1:184678800-184710800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:184685000-184721800	Weak transcription	Fetal Heart	heart
17	chr1:184685400-184722800	Weak transcription	Ovary	ovary
18	chr1:184685600-184706000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:184685600-184711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:184685600-184714400	Weak transcription	Brain Substantia Nigra	brain
21	chr1:184685600-184721000	Weak transcription	Right Ventricle	heart
22	chr1:184685600-184722600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:184685800-184707000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:184685800-184715000	Weak transcription	Small Intestine	intestine
25	chr1:184686200-184722600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:184686400-184715600	Weak transcription	Colonic Mucosa	Colon
27	chr1:184688800-184714200	Weak transcription	Fetal Brain Male	brain
28	chr1:184689200-184709600	Weak transcription	NHLF	lung
29	chr1:184690400-184721800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:184691600-184706800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:184692000-184707200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:184692200-184707000	Strong transcription	Fetal Thymus	thymus
33	chr1:184692800-184707000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:184694000-184706800	Strong transcription	Adipose Nuclei	Adipose
35	chr1:184694000-184707000	Strong transcription	Placenta	Placenta
36	chr1:184695200-184715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:184695400-184714800	Weak transcription	HepG2	liver
38	chr1:184696000-184705800	Weak transcription	Hela-S3	cervix
39	chr1:184696600-184706800	Strong transcription	Liver	Liver
40	chr1:184696800-184706800	Strong transcription	Osteobl	bone
41	chr1:184697400-184706800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:184697400-184707000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:184697800-184706800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:184698200-184722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:184698400-184715000	Weak transcription	Fetal Lung	lung
46	chr1:184699400-184706200	Strong transcription	Fetal Intestine Large	intestine
47	chr1:184699400-184715200	Weak transcription	HUVEC	blood vessel
48	chr1:184699600-184706000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:184699800-184707000	Strong transcription	Dnd41	blood
50	chr1:184699800-184710800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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