Variant report

Variant	rs6794907
Chromosome Location	chr3:143566025-143566026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10513218	1.00[CHB][hapmap]
rs1394398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1504603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1504604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1995529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1995530	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2011297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2011303	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2361205	0.85[ASN][1000 genomes]
rs2885195	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4499594	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56220620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56407400	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57718888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58887384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58921154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59306133	1.00[ASN][1000 genomes]
rs60249173	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60523819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60550983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6768399	1.00[CHB][hapmap]
rs6768702	0.93[ASN][1000 genomes]
rs6780027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73869037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869039	0.85[ASN][1000 genomes]
rs73869041	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869049	1.00[ASN][1000 genomes]
rs73869050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871826	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871827	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7434217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7613146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7637640	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7653164	1.00[CHB][hapmap]
rs9824974	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9836851	0.93[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143558400-143566600	Weak transcription	Esophagus	oesophagus
2	chr3:143559800-143566400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:143559800-143566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:143560200-143566600	Weak transcription	Small Intestine	intestine
5	chr3:143562200-143566600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:143563200-143567600	Active TSS	GM12878-XiMat	blood
7	chr3:143563800-143566400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:143564400-143566200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:143564400-143566400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:143565000-143566600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:143565200-143566200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:143565200-143566200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:143565200-143566400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:143565200-143567400	Active TSS	Placenta	Placenta
15	chr3:143565200-143567400	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:143565400-143567600	Active TSS	Brain Hippocampus Middle	brain
17	chr3:143565400-143567600	Active TSS	Stomach Smooth Muscle	stomach
18	chr3:143565400-143567600	Active TSS	NHDF-Ad	bronchial
19	chr3:143565800-143566200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:143565800-143566200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:143565800-143566200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr3:143565800-143566200	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr3:143565800-143566200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr3:143565800-143566200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:143565800-143566200	Enhancers	Colonic Mucosa	Colon
26	chr3:143565800-143566200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr3:143565800-143566200	Flanking Active TSS	Fetal Lung	lung
28	chr3:143565800-143566200	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:143565800-143566400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:143565800-143566400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:143565800-143566400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr3:143565800-143566400	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:143565800-143566400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:143565800-143566400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:143565800-143566400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:143565800-143566400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr3:143565800-143566400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr3:143565800-143566400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:143565800-143566600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:143565800-143567000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr3:143565800-143567400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:143565800-143567400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:143565800-143567400	Active TSS	Liver	Liver
44	chr3:143565800-143567400	Active TSS	NHLF	lung
45	chr3:143565800-143567600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:143565800-143567600	Active TSS	Primary T cells fromperipheralblood	blood
47	chr3:143565800-143567600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:143565800-143567600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:143565800-143567600	Active TSS	Duodenum Mucosa	Duodenum
50	chr3:143565800-143567600	Active TSS	Duodenum Smooth Muscle	Duodenum

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