Variant report

Variant	rs9828279
Chromosome Location	chr3:42616297-42616298
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42614904..42616729-chr3:42673460..42675829,2	K562	blood:

Variant related genes	Relation type
ENSG00000114857	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13064311	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13066173	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13066333	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs168138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171057	0.80[ASN][1000 genomes]
rs2068278	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271181	0.88[ASN][1000 genomes]
rs2271184	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271187	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284305	0.96[ASN][1000 genomes]
rs237064	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2940407	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095258	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339656	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339720	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs339721	0.92[ASN][1000 genomes]
rs339724	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339729	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339735	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342523	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342524	0.82[ASN][1000 genomes]
rs342526	0.84[ASN][1000 genomes]
rs342534	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs342535	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342538	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs383937	0.96[ASN][1000 genomes]
rs3888651	0.94[ASN][1000 genomes]
rs398743	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60994254	0.94[ASN][1000 genomes]
rs612362	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs637852	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs638904	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651180	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654761	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs663258	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs664813	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs665206	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704982	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs807863	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs82755	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311323	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9813479	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819563	0.86[AMR][1000 genomes];0.85[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9828279	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:42598200-42616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:42602800-42616800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
6	chr3:42603400-42616600	Weak transcription	Fetal Brain Male	brain
7	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
8	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
9	chr3:42604400-42616800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:42604600-42622400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:42605000-42621400	Weak transcription	HMEC	breast
12	chr3:42605200-42622400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:42607800-42621600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
15	chr3:42608000-42623000	Weak transcription	Gastric	stomach
16	chr3:42608600-42621400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
18	chr3:42609000-42621600	Weak transcription	NHLF	lung
19	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
20	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
21	chr3:42609200-42621200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:42609200-42621600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:42609200-42621600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:42609200-42621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:42609200-42622400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:42609400-42616400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:42609400-42616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:42610000-42622000	Weak transcription	Osteobl	bone
30	chr3:42610400-42622600	Weak transcription	Right Ventricle	heart
31	chr3:42610600-42622200	Weak transcription	NH-A	brain
32	chr3:42610600-42623000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:42610800-42616400	Weak transcription	Brain Anterior Caudate	brain
34	chr3:42611000-42617000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:42611000-42621800	Weak transcription	Liver	Liver
36	chr3:42611200-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:42611200-42622000	Weak transcription	Brain Substantia Nigra	brain
38	chr3:42611400-42616600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:42611400-42616600	Weak transcription	NHDF-Ad	bronchial
40	chr3:42611400-42621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:42611400-42622800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:42611600-42616400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:42611600-42616800	Weak transcription	HUVEC	blood vessel
44	chr3:42611600-42619600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:42611600-42621200	Weak transcription	HepG2	liver
46	chr3:42611600-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:42611600-42622800	Weak transcription	Ovary	ovary
48	chr3:42611800-42616400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:42611800-42616400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:42611800-42621600	Weak transcription	Adipose Nuclei	Adipose

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