Variant report

Variant	rs10942946
Chromosome Location	chr5:80589998-80589999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80562714..80564322-chr5:80589942..80591670,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10514218	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11739833	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11739834	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11740916	1.00[ASN][1000 genomes]
rs11743842	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11743849	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11745275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749113	0.93[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11953113	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11957137	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12516089	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517538	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518716	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523578	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878594	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878597	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067803	1.00[ASN][1000 genomes]
rs56206535	0.82[AMR][1000 genomes]
rs62365025	0.82[EUR][1000 genomes]
rs62365031	1.00[ASN][1000 genomes]
rs62365032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365038	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365866	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365867	1.00[ASN][1000 genomes]
rs72771170	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10942946	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx
rs10942946	CTC-281B15.1	cis	lung	GTEx
rs10942946	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs10942946	CTC-281B15.1	cis	Thyroid	GTEx
rs10942946	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs10942946	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10942946	CTC-281B15.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10942946	CTC-281B15.1	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80572000-80595200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:80578800-80595200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80581600-80595800	Weak transcription	Small Intestine	intestine
4	chr5:80584200-80595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:80584400-80595000	Weak transcription	NH-A	brain
6	chr5:80586400-80595000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:80586400-80595000	Weak transcription	Hela-S3	cervix
8	chr5:80586800-80595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:80587000-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:80587000-80595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:80587400-80590200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:80587600-80591400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:80588000-80595000	Weak transcription	Osteobl	bone
14	chr5:80588000-80595200	Weak transcription	A549	lung
15	chr5:80588200-80594600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:80588200-80594600	Weak transcription	Ovary	ovary
17	chr5:80588200-80595000	Weak transcription	NHLF	lung
18	chr5:80588200-80595200	Weak transcription	Right Atrium	heart
19	chr5:80588200-80596400	Weak transcription	Right Ventricle	heart
20	chr5:80588400-80593000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:80588400-80593800	Weak transcription	HSMMtube	muscle
22	chr5:80588400-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:80588400-80595200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:80588400-80595200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:80588400-80595800	Weak transcription	Left Ventricle	heart
28	chr5:80588400-80596400	Weak transcription	Psoas Muscle	Psoas
29	chr5:80588600-80593200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:80588600-80593200	Weak transcription	Liver	Liver
31	chr5:80588600-80596200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:80588800-80590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:80588800-80590800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:80589000-80591000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:80589200-80593200	Weak transcription	Fetal Heart	heart
36	chr5:80589400-80595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:80589600-80590400	Weak transcription	Fetal Lung	lung
38	chr5:80589600-80590800	Weak transcription	Fetal Kidney	kidney
39	chr5:80589600-80595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:80589600-80595000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:80589600-80595000	Weak transcription	Brain Substantia Nigra	brain
42	chr5:80589600-80595200	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:80589600-80595800	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:80589800-80595000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:80589800-80595200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:80589800-80595200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:80589800-80596000	Weak transcription	Fetal Intestine Large	intestine

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