Variant report

Variant	rs2333716
Chromosome Location	chr1:184707353-184707354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184705153..184707744-chr1:184942725..184944472,2	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];0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1046239	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061508	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10752941	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797987	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911640	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911644	0.87[GIH][hapmap]
rs12032144	0.86[EUR][1000 genomes]
rs12043236	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12071631	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124714	0.87[EUR][1000 genomes]
rs12124929	0.87[GIH][hapmap]
rs12133674	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12567225	0.87[GIH][hapmap]
rs12567226	0.87[GIH][hapmap]
rs2024765	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2024767	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]
rs2207733	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2333715	0.87[GIH][hapmap]
rs35478695	0.86[EUR][1000 genomes]
rs3736757	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];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3895196	0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4469687	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4498770	0.81[EUR][1000 genomes]
rs4651230	0.87[GIH][hapmap]
rs6663178	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6677073	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726427	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7523023	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7525074	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs861575	0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs861577	0.87[ASN][1000 genomes]
rs861578	0.88[GIH][hapmap]
rs861579	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs861581	0.88[GIH][hapmap]
rs861582	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9425339	0.81[ASN][1000 genomes]
rs9425341	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425343	0.87[GIH][hapmap]
rs9425633	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425634	0.83[EUR][1000 genomes]
rs9425635	0.84[EUR][1000 genomes]
rs9658937	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9661314	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs971080	0.86[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
rs2333716	EDEM3	cis	Artery Tibial	GTEx
rs2333716	EDEM3	cis	Esophagus Muscularis	GTEx
rs2333716	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs2333716	EDEM3	cis	Nerve Tibial	GTEx
rs2333716	PRG4	cis	parietal	SCAN
rs2333716	PTRF	trans	cerebellum	SCAN

Chromatin state (count:106 , 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	chr1:184661200-184707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:184671200-184707400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:184674600-184723000	Weak transcription	Aorta	Aorta
6	chr1:184677600-184723200	Weak transcription	Lung	lung
7	chr1:184678800-184710800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:184685000-184721800	Weak transcription	Fetal Heart	heart
9	chr1:184685400-184722800	Weak transcription	Ovary	ovary
10	chr1:184685600-184711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:184685600-184714400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:184685600-184721000	Weak transcription	Right Ventricle	heart
13	chr1:184685600-184722600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:184685800-184715000	Weak transcription	Small Intestine	intestine
15	chr1:184686200-184722600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:184686400-184715600	Weak transcription	Colonic Mucosa	Colon
17	chr1:184688800-184714200	Weak transcription	Fetal Brain Male	brain
18	chr1:184689200-184709600	Weak transcription	NHLF	lung
19	chr1:184690400-184721800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:184695200-184715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:184695400-184714800	Weak transcription	HepG2	liver
22	chr1:184698200-184722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:184698400-184715000	Weak transcription	Fetal Lung	lung
24	chr1:184699400-184715200	Weak transcription	HUVEC	blood vessel
25	chr1:184699800-184710800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:184699800-184711600	Weak transcription	Gastric	stomach
27	chr1:184699800-184711600	Weak transcription	Thymus	Thymus
28	chr1:184699800-184722200	Weak transcription	Fetal Stomach	stomach
29	chr1:184700000-184711000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:184700000-184711600	Weak transcription	Psoas Muscle	Psoas
31	chr1:184701000-184714400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:184701600-184707600	Weak transcription	Stomach Mucosa	stomach
33	chr1:184701600-184721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:184701800-184715000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:184702000-184712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:184702200-184709000	Weak transcription	Fetal Brain Female	brain
37	chr1:184702200-184712000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:184702200-184714800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:184702200-184721800	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:184702200-184721800	Weak transcription	NH-A	brain
41	chr1:184702200-184722200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:184702600-184712200	Weak transcription	HMEC	breast
43	chr1:184702600-184712600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:184702600-184715000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:184703000-184715400	Weak transcription	HSMMtube	muscle
46	chr1:184703200-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:184703200-184722800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:184703400-184710800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:184703400-184714200	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:184703400-184721400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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