Variant report

Variant	rs807863
Chromosome Location	chr3:42629490-42629491
allele	A/G
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	POLR2A	chr3:42629326-42629642	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
2	chr3:42617574..42619731-chr3:42628804..42631519,2	MCF-7	breast:

Variant related genes	Relation type
SS18L2	TF binding region
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs13064311	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066173	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13066333	0.84[ASN][1000 genomes]
rs168138	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2068278	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271181	0.85[ASN][1000 genomes]
rs2271184	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271187	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284305	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs237064	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2940407	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3095258	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339656	0.92[ASN][1000 genomes]
rs339720	0.86[ASN][1000 genomes]
rs339721	0.88[ASN][1000 genomes]
rs339724	0.84[ASN][1000 genomes]
rs339729	0.88[ASN][1000 genomes]
rs339735	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342523	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs342526	0.81[ASN][1000 genomes]
rs342534	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs342535	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342538	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs383937	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3888651	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs398743	0.92[ASN][1000 genomes]
rs60994254	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs612362	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs637852	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs638904	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651180	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654761	0.88[ASN][1000 genomes]
rs663258	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs664813	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs665206	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704982	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs82755	0.90[ASN][1000 genomes]
rs9311323	0.90[ASN][1000 genomes]
rs9311324	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813479	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819563	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828279	0.86[EUR][1000 genomes];0.96[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
rs807863	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624200-42631400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42624200-42631600	Weak transcription	HSMMtube	muscle
3	chr3:42624400-42629800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:42624400-42629800	Weak transcription	NHEK	skin
5	chr3:42624400-42631200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:42624400-42631200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:42624400-42631200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:42624400-42631400	Weak transcription	Liver	Liver
9	chr3:42624400-42631400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:42624400-42631400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:42624600-42631200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:42624600-42631400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:42624600-42631400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:42624600-42631400	Weak transcription	Fetal Brain Male	brain
16	chr3:42624600-42631400	Weak transcription	A549	lung
17	chr3:42624800-42630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:42624800-42631400	Weak transcription	Primary B cells from cord blood	blood
19	chr3:42624800-42631400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:42624800-42631400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:42624800-42631400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:42624800-42631400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:42624800-42631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:42624800-42631600	Weak transcription	Gastric	stomach
25	chr3:42625000-42630200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:42625000-42631000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:42625000-42631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:42625000-42631200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:42625000-42631200	Weak transcription	GM12878-XiMat	blood
30	chr3:42625000-42631400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:42625000-42631400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:42625000-42631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:42625000-42631400	Weak transcription	Fetal Intestine Small	intestine
34	chr3:42625000-42631600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:42625200-42631400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:42625200-42631600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:42625400-42631400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:42625400-42631400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:42625600-42631200	Weak transcription	Dnd41	blood
40	chr3:42625600-42631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:42625600-42631400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:42628000-42631200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:42628800-42631600	Weak transcription	NHLF	lung
44	chr3:42629000-42631200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:42629400-42630000	Weak transcription	HMEC	breast

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