Variant report

Variant	rs13009270
Chromosome Location	chr2:172402537-172402538
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172397977..172400681-chr2:172402000..172404841,3	K562	blood:
2	chr2:172401098..172402714-chr2:172409540..172411685,2	K562	blood:
3	chr2:172401705..172405203-chr2:172412295..172415295,3	K562	blood:
4	chr2:172381109..172383253-chr2:172401135..172403233,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCAF17-5	chr2:172402329-172405155	NONHSAT075473

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060248	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs11687075	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617339	0.97[ASN][1000 genomes]
rs12617802	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12621138	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs12692964	0.85[EUR][1000 genomes]
rs12692965	0.85[EUR][1000 genomes]
rs13024499	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17222606	0.82[CEU][hapmap]
rs17288182	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288294	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35050777	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806562	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3806563	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3806564	0.85[EUR][1000 genomes]
rs3806565	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs3806566	0.85[EUR][1000 genomes]
rs66572658	0.85[EUR][1000 genomes]
rs66818940	0.85[EUR][1000 genomes]
rs66975464	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704600	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6726306	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67339714	0.85[EUR][1000 genomes]
rs6751899	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884409	0.88[CEU][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13009270	CYBRD1	cis	Whole Blood	GTEx
rs13009270	CYBRD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172381000-172410400	Weak transcription	Fetal Thymus	thymus
2	chr2:172381200-172404400	Weak transcription	Right Atrium	heart
3	chr2:172381200-172407200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:172381200-172410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:172381400-172405400	Weak transcription	Fetal Heart	heart
6	chr2:172386400-172419800	Weak transcription	Lung	lung
7	chr2:172387200-172413800	Weak transcription	Spleen	Spleen
8	chr2:172388000-172411400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:172388200-172411000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:172388400-172411800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:172388600-172412400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:172388800-172403200	Weak transcription	Small Intestine	intestine
13	chr2:172388800-172407400	Weak transcription	HSMM	muscle
14	chr2:172388800-172410400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:172388800-172411000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:172388800-172413800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:172388800-172413800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:172388800-172414800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:172388800-172414800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:172389000-172404000	Weak transcription	NH-A	brain
21	chr2:172389000-172411000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:172392400-172412200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:172394000-172411200	Weak transcription	NHLF	lung
24	chr2:172396600-172408200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:172396600-172414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:172397000-172410200	Weak transcription	Placenta	Placenta
27	chr2:172397600-172405400	Strong transcription	HSMMtube	muscle
28	chr2:172397800-172403000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:172398200-172408400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:172398200-172414000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:172398400-172411200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:172399400-172407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:172399400-172409400	Weak transcription	NHEK	skin
34	chr2:172399400-172410400	Weak transcription	Right Ventricle	heart
35	chr2:172399400-172411000	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:172399600-172409600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:172400000-172402600	Weak transcription	Aorta	Aorta
38	chr2:172400000-172402600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:172400000-172402600	Weak transcription	GM12878-XiMat	blood
40	chr2:172400000-172403400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:172400000-172403800	Weak transcription	Osteobl	bone
42	chr2:172400000-172409800	Weak transcription	K562	blood
43	chr2:172400000-172410200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:172400000-172410200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:172400000-172410200	Weak transcription	Ovary	ovary
46	chr2:172400000-172410400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:172400000-172410400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:172400000-172410400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:172400000-172410400	Weak transcription	Left Ventricle	heart
50	chr2:172400000-172410400	Weak transcription	Stomach Smooth Muscle	stomach

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