Variant report

Variant	rs2294408
Chromosome Location	chr1:209973549-209973550
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	chr1:209956612..209959583-chr1:209971561..209974310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1005287	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160411	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12403599	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015218	0.81[AFR][1000 genomes]
rs17015224	0.81[AFR][1000 genomes]
rs17015226	0.81[AFR][1000 genomes]
rs17015250	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2005982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073485	0.81[AFR][1000 genomes]
rs2073486	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073487	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235375	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236909	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357229	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58637469	0.81[AFR][1000 genomes]
rs59043219	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6659549	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694552	0.81[AFR][1000 genomes]
rs7545538	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545542	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552506	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs926347	0.81[AFR][1000 genomes]
rs926348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
3	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
5	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
6	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:209965800-209974600	Weak transcription	Small Intestine	intestine
15	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
17	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:209966200-209974600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:209968400-209975000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:209968600-209974200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:209968800-209974600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:209969000-209976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:209969000-209978600	Weak transcription	Lung	lung
24	chr1:209970000-209975400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:209971000-209974800	Genic enhancers	NHEK	skin
26	chr1:209971000-209976000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:209971200-209974200	Genic enhancers	HMEC	breast
28	chr1:209971200-209974600	Weak transcription	Fetal Heart	heart
29	chr1:209971800-209974400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:209972000-209973600	Strong transcription	Pancreas	Pancrea
31	chr1:209972000-209974000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:209972000-209974200	Strong transcription	Fetal Intestine Large	intestine
33	chr1:209972000-209978400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:209972000-209978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:209972400-209974600	Strong transcription	Fetal Intestine Small	intestine
36	chr1:209972400-209974800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:209972600-209973600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:209972600-209974600	Weak transcription	Stomach Mucosa	stomach
39	chr1:209972600-209974800	Strong transcription	Placenta	Placenta
40	chr1:209972800-209974000	Enhancers	Liver	Liver
41	chr1:209973200-209973600	Weak transcription	Left Ventricle	heart
42	chr1:209973200-209975400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:209973200-209976000	Weak transcription	Esophagus	oesophagus
44	chr1:209973200-209976200	Weak transcription	Gastric	stomach
45	chr1:209973400-209973800	Weak transcription	HUVEC	blood vessel

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