Variant report

Variant	rs2483604
Chromosome Location	chr10:116382644-116382645
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116380101..116382698-chr10:116387153..116390968,3	MCF-7	breast:
2	chr10:116381677..116383578-chr10:116393467..116395747,2	MCF-7	breast:
3	chr10:116310031..116311847-chr10:116382346..116385171,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2483602	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483605	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483608	1.00[AMR][1000 genomes]
rs2483611	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497668	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2497669	0.87[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497670	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497674	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497675	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2497676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2483604	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116372000-116383600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:116376400-116383000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:116378200-116385000	Enhancers	Right Atrium	heart
4	chr10:116378800-116382800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:116378800-116383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:116378800-116391200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:116379400-116383000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:116379600-116382800	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:116379600-116383600	Weak transcription	Aorta	Aorta
10	chr10:116379600-116383600	Enhancers	Fetal Heart	heart
11	chr10:116380000-116384200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:116381200-116385000	Enhancers	Left Ventricle	heart
13	chr10:116381400-116383400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:116381400-116385200	Enhancers	Stomach Mucosa	stomach
15	chr10:116381800-116383400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:116381800-116383400	Enhancers	Ovary	ovary
17	chr10:116382000-116383400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr10:116382000-116384000	Weak transcription	Pancreas	Pancrea
19	chr10:116382000-116384400	Enhancers	Gastric	stomach
20	chr10:116382000-116385000	Weak transcription	Right Ventricle	heart
21	chr10:116382000-116385600	Enhancers	HepG2	liver
22	chr10:116382200-116383600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr10:116382200-116383600	Enhancers	Fetal Kidney	kidney
24	chr10:116382200-116384000	Enhancers	Adipose Nuclei	Adipose
25	chr10:116382200-116384200	Weak transcription	Esophagus	oesophagus
26	chr10:116382200-116384400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:116382200-116384400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr10:116382200-116384400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr10:116382200-116385000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr10:116382400-116383000	Enhancers	Hela-S3	cervix
31	chr10:116382400-116383200	Enhancers	Brain Hippocampus Middle	brain
32	chr10:116382400-116383200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr10:116382400-116383200	Enhancers	Fetal Lung	lung
34	chr10:116382400-116383200	Enhancers	Lung	lung
35	chr10:116382400-116383200	Enhancers	A549	lung
36	chr10:116382400-116383200	Enhancers	HSMM	muscle
37	chr10:116382400-116383400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:116382400-116383400	Enhancers	Brain Anterior Caudate	brain
39	chr10:116382400-116383800	Enhancers	Duodenum Mucosa	Duodenum
40	chr10:116382400-116384000	Enhancers	Fetal Intestine Small	intestine
41	chr10:116382400-116384200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:116382400-116384200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:116382400-116384200	Enhancers	Colon Smooth Muscle	Colon
44	chr10:116382400-116384400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr10:116382400-116384400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr10:116382400-116384400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr10:116382400-116384400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:116382400-116384400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:116382400-116384400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr10:116382400-116384400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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