Variant report

Variant	rs2290976
Chromosome Location	chr3:42708632-42708633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42693104..42694831-chr3:42707360..42709210,2	MCF-7	breast:
2	chr3:42707323..42709990-chr3:42711723..42713357,2	K562	blood:
3	chr3:42707503..42709270-chr3:42712561..42714862,2	MCF-7	breast:
4	chr17:59434029..59435903-chr3:42707935..42710633,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13064597	0.94[EUR][1000 genomes]
rs13085143	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs13086680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13100261	0.90[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs339705	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs339708	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34077739	0.90[EUR][1000 genomes]
rs34196076	0.90[EUR][1000 genomes]
rs34243788	0.93[EUR][1000 genomes]
rs34721465	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35384559	0.93[EUR][1000 genomes]
rs3733059	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	0.85[EUR][1000 genomes]
rs58645732	0.93[EUR][1000 genomes]
rs66933062	0.99[EUR][1000 genomes]
rs67174294	0.94[EUR][1000 genomes]
rs6790204	0.90[CEU][hapmap]
rs6797491	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs6797545	0.90[CEU][hapmap]
rs7614219	0.89[CEU][hapmap]
rs7616701	0.89[CEU][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290976	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
3	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:42701400-42708800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:42701600-42709000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:42701600-42709000	Weak transcription	Aorta	Aorta
8	chr3:42701800-42709200	Weak transcription	NHDF-Ad	bronchial
9	chr3:42702000-42709000	Weak transcription	Osteobl	bone
10	chr3:42702200-42709200	Weak transcription	Gastric	stomach
11	chr3:42702600-42709000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:42703800-42709200	Weak transcription	Placenta	Placenta
13	chr3:42705400-42709400	Weak transcription	Brain Germinal Matrix	brain
14	chr3:42705600-42709200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:42705600-42709200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:42705600-42709200	Weak transcription	Fetal Brain Female	brain
17	chr3:42705600-42709400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:42705800-42709000	Weak transcription	Lung	lung
19	chr3:42706200-42710600	Enhancers	Fetal Muscle Leg	muscle
20	chr3:42706400-42709000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:42706600-42708800	Weak transcription	NHLF	lung
22	chr3:42706600-42709800	Enhancers	Esophagus	oesophagus
23	chr3:42706600-42710000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:42706800-42708800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:42706800-42709400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:42706800-42710200	Enhancers	Right Ventricle	heart
27	chr3:42706800-42710800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:42707000-42708800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:42707000-42709000	Weak transcription	Spleen	Spleen
30	chr3:42707000-42709400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:42707000-42709800	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:42707000-42710200	Enhancers	Left Ventricle	heart
33	chr3:42707200-42708800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:42707200-42710000	Enhancers	Colon Smooth Muscle	Colon
35	chr3:42707200-42710000	Enhancers	Fetal Heart	heart
36	chr3:42707600-42708800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:42707600-42709200	Enhancers	Adipose Nuclei	Adipose
38	chr3:42707600-42709600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr3:42707600-42709600	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:42707800-42709800	Enhancers	Psoas Muscle	Psoas
41	chr3:42707800-42710200	Enhancers	HSMMtube	muscle
42	chr3:42708000-42709800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:42708000-42710000	Enhancers	Ovary	ovary
44	chr3:42708000-42710200	Enhancers	Stomach Smooth Muscle	stomach
45	chr3:42708000-42710400	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:42708000-42710400	Enhancers	Brain Hippocampus Middle	brain
47	chr3:42708000-42710400	Enhancers	Right Atrium	heart
48	chr3:42708200-42710000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:42708200-42710200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:42708400-42709800	Enhancers	Cortex derived primary cultured neurospheres	brain

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