Variant report

Variant	rs2542940
Chromosome Location	chr2:172412510-172412511
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	chr2:172401705..172405203-chr2:172412295..172415295,3	K562	blood:
3	chr2:172411652..172413746-chr2:172420952..172422723,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11684782	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12692966	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs2542932	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2542933	0.89[AFR][1000 genomes]
rs2542938	0.83[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs2542941	0.80[MEX][hapmap]
rs2674485	0.93[ASW][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585194	0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap]
rs950163	0.80[MEX][hapmap]

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
rs2542940	CHRNA1	cis	parietal	SCAN
rs2542940	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr2:172388800-172413800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:172388800-172413800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:172388800-172414800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:172388800-172414800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:172396600-172414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:172398200-172414000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:172400000-172416400	Weak transcription	Gastric	stomach
10	chr2:172400200-172413800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:172406000-172413800	Weak transcription	Esophagus	oesophagus
12	chr2:172406200-172414400	Strong transcription	HSMMtube	muscle
13	chr2:172407200-172413600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:172407200-172414400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:172407600-172413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:172408400-172414400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:172409200-172413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:172409600-172412800	Strong transcription	NHDF-Ad	bronchial
19	chr2:172410000-172415600	Weak transcription	NHEK	skin
20	chr2:172410200-172413000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:172410400-172412600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:172410400-172412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:172410400-172412600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172410400-172412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:172410400-172412600	Strong transcription	Fetal Stomach	stomach
26	chr2:172410400-172412600	Strong transcription	Right Ventricle	heart
27	chr2:172410400-172412600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr2:172410400-172412800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:172410400-172413400	Strong transcription	Left Ventricle	heart
30	chr2:172410400-172413600	Strong transcription	Adipose Nuclei	Adipose
31	chr2:172410400-172413600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:172410600-172412800	Weak transcription	Thymus	Thymus
33	chr2:172410600-172413200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:172410800-172413000	Strong transcription	Fetal Lung	lung
35	chr2:172410800-172413800	Weak transcription	Fetal Thymus	thymus
36	chr2:172410800-172415800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:172411000-172412600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:172411000-172412600	Strong transcription	Osteobl	bone
39	chr2:172411000-172412800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:172411000-172412800	Strong transcription	Brain Hippocampus Middle	brain
41	chr2:172411000-172412800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:172411000-172413000	Strong transcription	Aorta	Aorta
43	chr2:172411000-172413600	Weak transcription	Placenta	Placenta
44	chr2:172411000-172414200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:172411200-172412600	Strong transcription	HUVEC	blood vessel
46	chr2:172411200-172412800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:172411200-172412800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr2:172411200-172412800	Strong transcription	NHLF	lung
49	chr2:172411200-172413600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:172411400-172412800	Strong transcription	Ovary	ovary

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