Variant report

Variant	rs2794397
Chromosome Location	chr1:225881585-225881586
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	chr1:225839717..225843570-chr1:225880130..225881899,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ENAH-3	chr1:225881094-225881613	NONHSAT009843

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1876083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615062	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2769686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2840947	0.90[AFR][1000 genomes]
rs2840951	0.90[AFR][1000 genomes]
rs2840954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840964	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9660779	0.89[AMR][1000 genomes];0.81[EUR][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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225865600-225888000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:225875200-225898600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:225877400-225882600	Enhancers	Osteobl	bone
4	chr1:225877800-225882400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr1:225878000-225882600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:225878000-225883000	Weak transcription	NHEK	skin
7	chr1:225878600-225882400	Enhancers	Adipose Nuclei	Adipose
8	chr1:225878600-225882800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:225878600-225884000	Enhancers	Right Atrium	heart
10	chr1:225878600-225885400	Enhancers	Left Ventricle	heart
11	chr1:225878800-225882800	Enhancers	Stomach Mucosa	stomach
12	chr1:225879000-225884200	Enhancers	Liver	Liver
13	chr1:225879000-225884400	Enhancers	HepG2	liver
14	chr1:225879400-225881800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:225879400-225882000	Weak transcription	Aorta	Aorta
16	chr1:225879400-225887000	Weak transcription	NHLF	lung
17	chr1:225879600-225881600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:225879600-225882000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:225879600-225882400	Enhancers	NH-A	brain
20	chr1:225880000-225881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:225880200-225881800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:225880200-225881800	Weak transcription	Ovary	ovary
23	chr1:225880200-225882200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:225880200-225883000	Weak transcription	NHDF-Ad	bronchial
25	chr1:225880400-225882800	Enhancers	Fetal Intestine Large	intestine
26	chr1:225880400-225883000	Enhancers	Fetal Lung	lung
27	chr1:225880400-225884200	Enhancers	A549	lung
28	chr1:225880800-225881800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:225880800-225882000	Weak transcription	Esophagus	oesophagus
30	chr1:225880800-225882200	Weak transcription	Lung	lung
31	chr1:225880800-225887800	Weak transcription	Spleen	Spleen
32	chr1:225881000-225882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:225881000-225882000	Weak transcription	Pancreas	Pancrea
34	chr1:225881000-225882000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225881000-225882200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:225881000-225882200	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:225881000-225882400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:225881000-225882400	Enhancers	Fetal Heart	heart
39	chr1:225881000-225882400	Enhancers	Hela-S3	cervix
40	chr1:225881000-225882800	Weak transcription	Gastric	stomach
41	chr1:225881000-225883000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:225881000-225883000	Enhancers	HUVEC	blood vessel
43	chr1:225881000-225883800	Weak transcription	Psoas Muscle	Psoas
44	chr1:225881000-225887200	Weak transcription	Right Ventricle	heart
45	chr1:225881200-225882000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:225881200-225882000	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:225881200-225883000	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:225881400-225881800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:225881400-225882000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:225881400-225882000	Weak transcription	Fetal Intestine Small	intestine

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