Variant report

Variant	rs1558936
Chromosome Location	chr2:172328450-172328451
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	CTCF	chr2:172328408-172328469	GM13976	blood:	n/a	n/a

Variant related genes	Relation type
DCAF17	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10445722	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10515933	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12151641	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17220419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17220440	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17220608	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17220657	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17220699	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17220734	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17221367	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17221402	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17221619	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17286415	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17286660	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1861899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1981788	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356781	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36112363	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731981	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731982	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3731983	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731985	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795998	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821084	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417688	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4458186	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4496302	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4522571	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4668385	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4668386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4668387	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56410960	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57099324	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58536060	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59960186	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60439518	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62181352	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62183467	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62183468	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183470	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62183471	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62183472	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183492	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183493	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62183494	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183495	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183497	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183498	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183499	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62183502	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62183503	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62183506	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183507	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183539	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433290	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433292	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713612	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6720250	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6740733	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6741806	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743290	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568037	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7572334	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7576894	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598137	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7606658	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9678149	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9678164	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9679537	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789572	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789596	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558936	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:172298400-172334400	Weak transcription	Small Intestine	intestine
4	chr2:172298400-172339400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172298600-172341400	Weak transcription	NHLF	lung
6	chr2:172300600-172338600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:172304800-172330000	Weak transcription	NH-A	brain
8	chr2:172304800-172338800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:172306800-172334000	Weak transcription	Psoas Muscle	Psoas
11	chr2:172307800-172341200	Weak transcription	Right Ventricle	heart
12	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart
13	chr2:172313400-172339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:172315000-172337400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:172315400-172329600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:172322800-172337800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:172324400-172340600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:172324600-172338200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:172324600-172340000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:172324800-172334800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:172324800-172334800	Strong transcription	Dnd41	blood
22	chr2:172324800-172337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:172324800-172340400	Strong transcription	Primary T cells from cord blood	blood
24	chr2:172324800-172341200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:172325000-172333200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:172325000-172340200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:172325200-172328800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:172325200-172329800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:172325200-172332200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:172325200-172332400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:172325200-172334800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:172325200-172335200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:172325200-172338000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:172325200-172338600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:172325200-172340000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:172325400-172328600	Strong transcription	Left Ventricle	heart
37	chr2:172325400-172328800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr2:172325400-172329000	Strong transcription	Fetal Stomach	stomach
39	chr2:172325400-172333400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:172325400-172334800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:172325600-172332000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:172325600-172334600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:172325800-172328800	Strong transcription	Liver	Liver
44	chr2:172325800-172331800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:172326400-172330400	Weak transcription	NHDF-Ad	bronchial
46	chr2:172327000-172331200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:172327000-172339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:172327000-172346800	Weak transcription	Colonic Mucosa	Colon
49	chr2:172327200-172329000	Weak transcription	HSMM	muscle
50	chr2:172327200-172329800	Weak transcription	Colon Smooth Muscle	Colon

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