Variant report

Variant	rs7640840
Chromosome Location	chr3:53908905-53908906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:53908860-53909010	GM12866	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53906924..53910795-chr3:53914021..53916121,3	MCF-7	breast:
3	chr3:53903830..53906738-chr3:53907491..53909258,2	MCF-7	breast:

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11130383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11562	0.83[AFR][1000 genomes]
rs12715465	1.00[AMR][1000 genomes]
rs13321898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322337	1.00[AMR][1000 genomes]
rs13434145	1.00[AMR][1000 genomes]
rs28409957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6782007	1.00[AMR][1000 genomes]
rs6785238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72556356	1.00[AMR][1000 genomes]
rs7614233	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7636496	1.00[AMR][1000 genomes]
rs7637908	1.00[AMR][1000 genomes]
rs9814675	1.00[AMR][1000 genomes]
rs9816010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818571	1.00[AMR][1000 genomes]
rs9823141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9830672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9835258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849610	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859937	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860224	1.00[AMR][1000 genomes]
rs9872403	1.00[AMR][1000 genomes]
rs9878250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
2	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
7	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
9	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
11	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
12	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
24	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
27	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:53893200-53914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:53893800-53912800	Strong transcription	Brain Anterior Caudate	brain
35	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:53894400-53914000	Strong transcription	Primary T cells from cord blood	blood
37	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus
38	chr3:53894800-53914200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:53894800-53914200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:53895000-53914000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:53895000-53914200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:53895000-53914400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:53895200-53913200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:53895200-53914200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:53895200-53914200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:53895200-53914200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:53895400-53913800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:53895600-53914200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:53895800-53913800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:53896200-53912800	Strong transcription	Brain Inferior Temporal Lobe	brain

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