Variant report

Variant	rs35384559
Chromosome Location	chr3:42689509-42689510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42671852..42674989-chr3:42686737..42692314,6	K562	blood:
2	chr3:42688509..42691154-chr3:42691239..42693774,3	MCF-7	breast:
3	chr3:42688256..42690363-chr3:42691600..42693510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114857	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13064597	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086680	0.91[EUR][1000 genomes]
rs13100261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.81[EUR][1000 genomes]
rs2290976	0.93[EUR][1000 genomes]
rs339708	0.91[EUR][1000 genomes]
rs34077739	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196076	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.90[EUR][1000 genomes]
rs35216140	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871059	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733059	0.93[EUR][1000 genomes]
rs3733061	0.91[EUR][1000 genomes]
rs3900780	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994846	1.00[ASN][1000 genomes]
rs56047094	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58645732	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[ASN][1000 genomes]
rs60535002	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66933062	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67174294	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583158	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67832425	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.83[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	1.00[ASN][1000 genomes]
rs68004576	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71323162	1.00[ASN][1000 genomes]
rs72864022	1.00[ASN][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[ASN][1000 genomes]
rs7616701	1.00[ASN][1000 genomes]
rs7623867	0.83[EUR][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	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
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35384559	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:42658400-42691400	Strong transcription	Dnd41	blood
4	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr3:42668800-42690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:42669000-42690600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
8	chr3:42669200-42692200	Strong transcription	Liver	Liver
9	chr3:42669400-42690600	Strong transcription	K562	blood
10	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
12	chr3:42669600-42690000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:42671000-42690800	Strong transcription	Placenta	Placenta
15	chr3:42671200-42690800	Strong transcription	NHDF-Ad	bronchial
16	chr3:42671200-42691400	Strong transcription	HSMM	muscle
17	chr3:42671200-42691600	Strong transcription	NH-A	brain
18	chr3:42671400-42689800	Strong transcription	Primary B cells from cord blood	blood
19	chr3:42671400-42690600	Strong transcription	Fetal Lung	lung
20	chr3:42671400-42692200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:42671400-42692200	Strong transcription	Adipose Nuclei	Adipose
22	chr3:42672000-42690600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr3:42672000-42691800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:42672600-42692200	Strong transcription	Fetal Brain Female	brain
25	chr3:42673200-42692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:42673600-42690400	Strong transcription	NHLF	lung
27	chr3:42674800-42692200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:42676600-42690000	Strong transcription	HepG2	liver
29	chr3:42676800-42690200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:42677000-42692800	Strong transcription	Fetal Stomach	stomach
31	chr3:42677600-42692600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:42680200-42690600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:42680600-42692400	Strong transcription	Fetal Intestine Small	intestine
34	chr3:42680800-42692200	Weak transcription	Right Atrium	heart
35	chr3:42681000-42690600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:42681000-42690600	Strong transcription	GM12878-XiMat	blood
37	chr3:42681200-42691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:42681400-42691400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:42682600-42690800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:42682800-42690600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:42682800-42690600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:42682800-42692200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:42683000-42690400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:42683200-42691000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:42683200-42692200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:42683600-42690000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:42683600-42690400	Strong transcription	HUVEC	blood vessel
48	chr3:42683800-42689600	Strong transcription	HSMMtube	muscle
49	chr3:42683800-42689800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:42683800-42690600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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