Variant report

Variant	rs3790399
Chromosome Location	chr1:169911840-169911841
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	chr1:169907968..169909649-chr1:169910615..169913475,2	K562	blood:
2	chr1:169909334..169912008-chr1:170041825..170044429,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075945	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10919256	0.81[ASN][1000 genomes]
rs10919258	0.85[ASN][1000 genomes]
rs10919259	0.83[ASN][1000 genomes]
rs12405525	0.83[ASN][1000 genomes]
rs12410352	0.83[ASN][1000 genomes]
rs12742961	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16862911	1.00[JPT][hapmap]
rs2205846	0.83[ASN][1000 genomes]
rs2272917	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2272918	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3817858	0.84[ASN][1000 genomes]
rs67274208	0.83[ASN][1000 genomes]
rs73026223	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1007190	chr1:169890542-169929582	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv997360	chr1:169892284-169946436	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1015110	chr1:169892661-169929582	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013271	chr1:169892661-169960549	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010007	chr1:169895282-169946436	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1003588	chr1:169895984-169946436	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998382	chr1:169899427-169929582	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1011978	chr1:169899427-169946436	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv997289	chr1:169899427-169960549	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1012520	chr1:169899427-169969444	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1003803	chr1:169901733-169929582	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1001670	chr1:169901733-169956450	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1004999	chr1:169901733-169960549	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1009843	chr1:169903077-169950341	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1012222	chr1:169903862-169950341	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:169885400-169913200	Weak transcription	Ovary	ovary
4	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:169886600-169915600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:169891000-169913200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:169901400-169913000	Weak transcription	Fetal Stomach	stomach
8	chr1:169901400-169913200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:169904000-169929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:169904000-169934800	Weak transcription	Fetal Heart	heart
11	chr1:169904000-169949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
13	chr1:169905200-169915400	Weak transcription	GM12878-XiMat	blood
14	chr1:169907800-169913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:169909200-169946000	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169909800-169913200	Weak transcription	Esophagus	oesophagus
17	chr1:169910000-169913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:169910000-169913200	Weak transcription	Lung	lung
19	chr1:169910200-169913200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:169910400-169946200	Weak transcription	Primary B cells from cord blood	blood
21	chr1:169910800-169912000	Enhancers	Hela-S3	cervix
22	chr1:169910800-169912400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:169911000-169912000	Enhancers	HUVEC	blood vessel
24	chr1:169911000-169912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:169911200-169912000	Enhancers	A549	lung
26	chr1:169911200-169912200	Enhancers	NHDF-Ad	bronchial
27	chr1:169911200-169914800	Weak transcription	Gastric	stomach
28	chr1:169911200-169948800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:169911400-169912000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:169911400-169912000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:169911400-169912000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:169911400-169912000	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:169911400-169912000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:169911400-169912000	Enhancers	NH-A	brain
35	chr1:169911400-169912000	Enhancers	NHLF	lung
36	chr1:169911400-169912000	Flanking Active TSS	Osteobl	bone
37	chr1:169911400-169912200	Strong transcription	Left Ventricle	heart
38	chr1:169911400-169912400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr1:169911400-169913200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:169911400-169913200	Weak transcription	Fetal Brain Female	brain
41	chr1:169911400-169914400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:169911400-169923000	Weak transcription	Liver	Liver
43	chr1:169911400-169946200	Weak transcription	Dnd41	blood
44	chr1:169911400-169948600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:169911600-169912000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:169911600-169912000	Enhancers	Small Intestine	intestine
47	chr1:169911600-169912000	Enhancers	HSMM	muscle
48	chr1:169911600-169913000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:169911600-169913200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:169911600-169913200	Weak transcription	Fetal Intestine Small	intestine

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