Variant report

Variant	rs67583158
Chromosome Location	chr3:42614596-42614597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42613871..42615893-chr3:42692209..42694692,2	K562	blood:
2	chr3:42611786..42615300-chr3:42621924..42624198,4	K562	blood:
3	chr3:42612219..42614700-chr3:42641488..42643709,2	MCF-7	breast:
4	chr3:42612205..42615201-chr3:42631564..42633106,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13064597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072295	0.82[EUR][1000 genomes]
rs13085143	1.00[ASN][1000 genomes]
rs13085695	0.82[EUR][1000 genomes]
rs13089845	0.82[EUR][1000 genomes]
rs13090902	0.82[EUR][1000 genomes]
rs13093680	0.82[EUR][1000 genomes]
rs13095447	0.82[EUR][1000 genomes]
rs13100261	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.97[EUR][1000 genomes]
rs17074662	0.82[EUR][1000 genomes]
rs17074673	0.82[EUR][1000 genomes]
rs17074674	0.82[EUR][1000 genomes]
rs17074693	0.82[EUR][1000 genomes]
rs2284303	0.82[EUR][1000 genomes]
rs2284304	0.82[EUR][1000 genomes]
rs2300057	0.82[EUR][1000 genomes]
rs2300058	0.82[EUR][1000 genomes]
rs2302352	0.82[EUR][1000 genomes]
rs33969824	0.82[EUR][1000 genomes]
rs339705	0.89[EUR][1000 genomes]
rs33984028	0.82[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.82[EUR][1000 genomes]
rs34687113	0.80[EUR][1000 genomes]
rs34762478	0.82[EUR][1000 genomes]
rs34801786	0.82[EUR][1000 genomes]
rs34852409	0.82[EUR][1000 genomes]
rs34977988	0.82[EUR][1000 genomes]
rs35216140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.82[EUR][1000 genomes]
rs35871059	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35890296	0.82[EUR][1000 genomes]
rs36033201	0.82[EUR][1000 genomes]
rs36043081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774401	0.82[EUR][1000 genomes]
rs3774402	0.82[EUR][1000 genomes]
rs3774404	0.82[EUR][1000 genomes]
rs3774407	0.82[EUR][1000 genomes]
rs3846058	0.82[EUR][1000 genomes]
rs3846059	0.82[EUR][1000 genomes]
rs3856737	0.82[EUR][1000 genomes]
rs3900780	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56797870	0.82[EUR][1000 genomes]
rs57259216	0.82[EUR][1000 genomes]
rs58645732	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.82[EUR][1000 genomes]
rs59914338	0.82[EUR][1000 genomes]
rs60232916	0.82[EUR][1000 genomes]
rs60348477	0.82[EUR][1000 genomes]
rs60535002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149998	0.82[EUR][1000 genomes]
rs6441928	0.82[EUR][1000 genomes]
rs66786953	0.81[EUR][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67059259	0.82[EUR][1000 genomes]
rs67174294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.80[EUR][1000 genomes]
rs6771105	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	0.82[EUR][1000 genomes]
rs6782164	0.82[EUR][1000 genomes]
rs67832425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788548	0.82[EUR][1000 genomes]
rs6790204	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793186	0.82[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6795296	0.82[EUR][1000 genomes]
rs6797491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028490	0.82[EUR][1000 genomes]
rs68071013	0.82[EUR][1000 genomes]
rs71323162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864022	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864072	0.82[EUR][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617403	0.82[EUR][1000 genomes]
rs7617736	0.82[EUR][1000 genomes]
rs7623867	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7624628	0.82[EUR][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
rs67583158	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 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	chr3:42594600-42615200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr3:42598000-42615600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:42598200-42616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42602800-42616800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
8	chr3:42603400-42616600	Weak transcription	Fetal Brain Male	brain
9	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
10	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
11	chr3:42604400-42615200	Weak transcription	Hela-S3	cervix
12	chr3:42604400-42616800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:42604600-42622400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:42605000-42621400	Weak transcription	HMEC	breast
15	chr3:42605200-42622400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:42605600-42615400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:42607800-42615200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:42607800-42615200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:42607800-42621600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
21	chr3:42608000-42623000	Weak transcription	Gastric	stomach
22	chr3:42608600-42621400	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
24	chr3:42609000-42621600	Weak transcription	NHLF	lung
25	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
26	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
27	chr3:42609200-42615400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:42609200-42616000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:42609200-42616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:42609200-42616200	Weak transcription	Fetal Kidney	kidney
31	chr3:42609200-42616200	Weak transcription	Placenta	Placenta
32	chr3:42609200-42621200	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:42609200-42621600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:42609200-42621600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:42609200-42621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:42609200-42622400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:42609400-42615200	Weak transcription	Primary B cells from cord blood	blood
38	chr3:42609400-42616400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:42609400-42616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:42610000-42622000	Weak transcription	Osteobl	bone
42	chr3:42610400-42622600	Weak transcription	Right Ventricle	heart
43	chr3:42610600-42615600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:42610600-42622200	Weak transcription	NH-A	brain
45	chr3:42610600-42623000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:42610800-42614800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:42610800-42616400	Weak transcription	Brain Anterior Caudate	brain
48	chr3:42611000-42614600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:42611000-42615200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:42611000-42615400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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