Variant report

Variant	rs2794394
Chromosome Location	chr1:225888437-225888438
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRP9-1	chr1:225888418-225888808	XLOC_000587
2	lnc-SRP9-1	chr1:225888431-225888808	XLOC_000587
3	lnc-SRP9-1	chr1:225888415-225888808	XLOC_000587
4	lnc-SRP9-1	chr1:225888306-225888808	ENSG00000227496.1

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2246539	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2615063	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2615066	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2639710	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2794393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794398	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35303986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61850656	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701838	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7512304	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7554842	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7555374	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225875200-225898600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:225882200-225889600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:225882400-225908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:225887000-225888600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:225887000-225888600	Enhancers	Fetal Stomach	stomach
6	chr1:225887000-225888800	Enhancers	HUVEC	blood vessel
7	chr1:225887000-225889000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:225887000-225889000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:225887000-225889200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:225887000-225889200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:225887000-225889200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:225887000-225889200	Enhancers	NHLF	lung
13	chr1:225887200-225888600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:225887200-225889200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:225887200-225889200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:225887200-225889400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:225887400-225888800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:225887600-225888800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:225887600-225888800	Flanking Active TSS	Hela-S3	cervix
20	chr1:225887600-225889600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:225887800-225890600	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr1:225888000-225889600	Active TSS	Psoas Muscle	Psoas
23	chr1:225888000-225890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:225888000-225891800	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:225888200-225889000	Flanking Active TSS	A549	lung
26	chr1:225888400-225888600	Flanking Active TSS	Aorta	Aorta
27	chr1:225888400-225888800	Flanking Active TSS	HMEC	breast
28	chr1:225888400-225888800	Flanking Active TSS	NHEK	skin
29	chr1:225888400-225889000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:225888400-225889000	Flanking Active TSS	HSMM	muscle
31	chr1:225888400-225889000	Flanking Active TSS	HSMMtube	muscle
32	chr1:225888400-225889200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:225888400-225889200	Enhancers	HepG2	liver
34	chr1:225888400-225889200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr1:225888400-225889600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:225888400-225889600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:225888400-225889600	Flanking Active TSS	NH-A	brain
38	chr1:225888400-225889600	Flanking Active TSS	Osteobl	bone
39	chr1:225888400-225899000	Weak transcription	Stomach Smooth Muscle	stomach

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