Variant report

Variant	rs2867946
Chromosome Location	chr1:56042151-56042152
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	chr1:56042144-56042235	HepG2	liver:	n/a	n/a
2	RAD21	chr1:56042029-56042217	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000234810	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4927254	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4927255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658576	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs904602	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2867946	PRKAR2A	trans	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56035400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus
3	chr1:56038200-56042200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:56038400-56042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:56039000-56045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:56039000-56045800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:56039000-56046000	Weak transcription	NHLF	lung
8	chr1:56039000-56046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:56039200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:56039200-56047200	Weak transcription	Psoas Muscle	Psoas
11	chr1:56039400-56045000	Weak transcription	HSMMtube	muscle
12	chr1:56039600-56043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:56039600-56046200	Weak transcription	NH-A	brain
14	chr1:56040600-56042200	Enhancers	Fetal Muscle Leg	muscle
15	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:56041000-56042200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:56041000-56042200	Enhancers	Brain Angular Gyrus	brain
18	chr1:56041000-56042200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:56041200-56042200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:56041200-56042200	Enhancers	Brain Hippocampus Middle	brain
21	chr1:56041200-56042200	Enhancers	Brain Substantia Nigra	brain
22	chr1:56041200-56042200	Enhancers	Left Ventricle	heart
23	chr1:56041200-56042200	Enhancers	Right Atrium	heart
24	chr1:56041400-56042200	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:56041600-56044400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:56041800-56042200	Enhancers	Lung	lung
27	chr1:56041800-56042200	Enhancers	Pancreas	Pancrea
28	chr1:56041800-56045000	Weak transcription	Osteobl	bone
29	chr1:56041800-56045200	Weak transcription	NHDF-Ad	bronchial
30	chr1:56042000-56042800	Weak transcription	Brain Germinal Matrix	brain
31	chr1:56042000-56043000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:56042000-56043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:56042000-56043400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:56042000-56043800	Weak transcription	Right Ventricle	heart
35	chr1:56042000-56044000	Weak transcription	Fetal Lung	lung
36	chr1:56042000-56044600	Weak transcription	HSMM	muscle
37	chr1:56042000-56045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:56042000-56046200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:56042000-56046400	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:56042000-56046600	Weak transcription	Brain Anterior Caudate	brain
41	chr1:56042000-56047400	Weak transcription	Placenta Amnion	Placenta Amnion

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