Variant report

Variant	rs10455
Chromosome Location	chr2:172411273-172411274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172284791..172287152-chr2:172410129..172412557,2	K562	blood:
2	chr2:172404878..172406408-chr2:172409162..172411788,2	K562	blood:
3	chr2:172401098..172402714-chr2:172409540..172411685,2	K562	blood:
4	chr2:172409708..172411658-chr2:172542910..172545058,2	K562	blood:
5	chr2:172172855..172175323-chr2:172409152..172411417,2	K562	blood:

Variant related genes	Relation type
ENSG00000077380	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11675373	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999785	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2111720	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs2542939	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542941	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2674490	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs950163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10455	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL
rs10455	CYBRD1	cis	lymphoblastoid	seeQTL
rs10455	CHRNA1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172386400-172419800	Weak transcription	Lung	lung
2	chr2:172387200-172413800	Weak transcription	Spleen	Spleen
3	chr2:172388000-172411400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:172388400-172411800	Weak transcription	Brain Substantia Nigra	brain
5	chr2:172388600-172412400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:172388800-172413800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:172388800-172413800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:172388800-172414800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:172388800-172414800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:172392400-172412200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:172396600-172414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:172398200-172414000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:172400000-172416400	Weak transcription	Gastric	stomach
14	chr2:172400200-172413800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:172406000-172413800	Weak transcription	Esophagus	oesophagus
16	chr2:172406200-172414400	Strong transcription	HSMMtube	muscle
17	chr2:172407200-172413600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:172407200-172414400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:172407600-172413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:172408200-172412400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:172408400-172414400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:172409200-172413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:172409600-172412800	Strong transcription	NHDF-Ad	bronchial
24	chr2:172410000-172415600	Weak transcription	NHEK	skin
25	chr2:172410200-172413000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:172410400-172412200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:172410400-172412400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:172410400-172412400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr2:172410400-172412600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:172410400-172412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:172410400-172412600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:172410400-172412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:172410400-172412600	Strong transcription	Fetal Stomach	stomach
34	chr2:172410400-172412600	Strong transcription	Right Ventricle	heart
35	chr2:172410400-172412600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:172410400-172412800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:172410400-172413400	Strong transcription	Left Ventricle	heart
38	chr2:172410400-172413600	Strong transcription	Adipose Nuclei	Adipose
39	chr2:172410400-172413600	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:172410600-172412200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:172410600-172412800	Weak transcription	Thymus	Thymus
42	chr2:172410600-172413200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr2:172410800-172412200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:172410800-172413000	Strong transcription	Fetal Lung	lung
45	chr2:172410800-172413800	Weak transcription	Fetal Thymus	thymus
46	chr2:172410800-172415800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:172411000-172411400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:172411000-172411400	Enhancers	HepG2	liver
49	chr2:172411000-172411400	Genic enhancers	K562	blood
50	chr2:172411000-172411800	Strong transcription	Brain Inferior Temporal Lobe	brain

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