Variant report

Variant	rs9827142
Chromosome Location	chr3:191116924-191116925
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	chr3:191109601..191112408-chr3:191114470..191116944,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13326246	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13434281	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17545865	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17754685	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17811727	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164237	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28368295	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28448537	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28502671	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28510847	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4677634	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687210	0.94[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9290985	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs980320	0.96[EUR][1000 genomes]
rs980321	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812544	0.86[AFR][1000 genomes]
rs9825936	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9826141	0.96[EUR][1000 genomes]
rs9839989	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844109	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855282	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868495	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9827142	CCDC50	cis	Esophagus Muscularis	GTEx
rs9827142	CCDC50	cis	Nerve Tibial	GTEx
rs9827142	FBXO45	cis	parietal	SCAN
rs9827142	CCDC50	cis	Thyroid	GTEx
rs9827142	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
11	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
12	chr3:191100200-191119600	Weak transcription	K562	blood
13	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
14	chr3:191100400-191117400	Weak transcription	Lung	lung
15	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
16	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
17	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
18	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:191101200-191117000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
22	chr3:191106800-191117200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:191107400-191117200	Weak transcription	HepG2	liver
24	chr3:191108000-191117400	Weak transcription	NHEK	skin
25	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
28	chr3:191109200-191117600	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:191110600-191117600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:191110600-191117600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:191111000-191117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:191111200-191118000	Weak transcription	Fetal Lung	lung
36	chr3:191111400-191117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:191111400-191117800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:191111400-191117800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:191112000-191118000	Strong transcription	Adipose Nuclei	Adipose
40	chr3:191112200-191118400	Strong transcription	NH-A	brain
41	chr3:191112400-191117200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:191113200-191118200	Weak transcription	Hela-S3	cervix
43	chr3:191113600-191118200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:191114200-191117200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:191114200-191117400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:191114200-191118000	Weak transcription	NHDF-Ad	bronchial
48	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
49	chr3:191114200-191119400	Weak transcription	NHLF	lung
50	chr3:191114400-191117600	Weak transcription	Rectal Mucosa Donor 29	rectum

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