Variant report

Variant	rs383937
Chromosome Location	chr3:42686001-42686002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42680050..42682875-chr3:42685577..42687486,2	K562	blood:
2	chr3:42641959..42644716-chr3:42685272..42688583,4	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000114857	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

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

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:42658400-42691400	Strong transcription	Dnd41	blood
6	chr3:42659000-42688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:42668000-42688200	Strong transcription	Fetal Thymus	thymus
8	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:42668800-42689200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:42668800-42690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:42669000-42690600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
13	chr3:42669200-42692200	Strong transcription	Liver	Liver
14	chr3:42669400-42690600	Strong transcription	K562	blood
15	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
17	chr3:42669600-42690000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:42671000-42690800	Strong transcription	Placenta	Placenta
20	chr3:42671200-42690800	Strong transcription	NHDF-Ad	bronchial
21	chr3:42671200-42691400	Strong transcription	HSMM	muscle
22	chr3:42671200-42691600	Strong transcription	NH-A	brain
23	chr3:42671400-42687600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:42671400-42689800	Strong transcription	Primary B cells from cord blood	blood
25	chr3:42671400-42690600	Strong transcription	Fetal Lung	lung
26	chr3:42671400-42692200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:42671400-42692200	Strong transcription	Adipose Nuclei	Adipose
28	chr3:42672000-42689000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:42672000-42689400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:42672000-42690600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr3:42672000-42691800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:42672200-42686400	Strong transcription	Brain Germinal Matrix	brain
33	chr3:42672200-42689000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:42672600-42692200	Strong transcription	Fetal Brain Female	brain
35	chr3:42673200-42688600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:42673200-42689000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:42673200-42692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:42673400-42686600	Strong transcription	Hela-S3	cervix
39	chr3:42673400-42688800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:42673600-42688600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:42673600-42689400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:42673600-42690400	Strong transcription	NHLF	lung
43	chr3:42673800-42688400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:42673800-42688800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr3:42674000-42688600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:42674000-42688800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:42674800-42692200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:42675000-42688400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:42676400-42688400	Strong transcription	Thymus	Thymus
50	chr3:42676600-42686800	Strong transcription	Primary T cells from cord blood	blood

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