Variant report

Variant	rs7549317
Chromosome Location	chr1:179860413-179860414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179853596..179856683-chr1:179859981..179861933,3	MCF-7	breast:
2	chr1:179858702..179861770-chr1:179862540..179865155,3	K562	blood:
3	chr1:179850437..179853668-chr1:179858763..179861436,4	K562	blood:

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1048418	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10494523	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10913894	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10913895	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10913905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119431	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12121694	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12126625	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301600	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61740391	0.94[EUR][1000 genomes]
rs6425596	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659939	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6673144	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72708661	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708662	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7531195	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7545581	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9726605	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179860800	Weak transcription	Stomach Mucosa	stomach
2	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
3	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
4	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:179853200-179861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
10	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
12	chr1:179853600-179861600	Strong transcription	Placenta	Placenta
13	chr1:179853800-179861200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:179853800-179863200	Strong transcription	Fetal Lung	lung
15	chr1:179854000-179865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
17	chr1:179854200-179863000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:179854200-179863000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:179854200-179866600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:179854600-179864800	Strong transcription	Fetal Intestine Large	intestine
22	chr1:179854800-179864200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:179855200-179864600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:179855600-179871600	Weak transcription	A549	lung
25	chr1:179856000-179866000	Strong transcription	Liver	Liver
26	chr1:179856200-179876800	Weak transcription	NHLF	lung
27	chr1:179857600-179860600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:179857600-179861400	Strong transcription	GM12878-XiMat	blood
29	chr1:179857600-179861600	Strong transcription	Primary T cells from cord blood	blood
30	chr1:179857600-179864000	Strong transcription	Dnd41	blood
31	chr1:179857600-179864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:179857600-179864800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:179857600-179864800	Strong transcription	Adipose Nuclei	Adipose
34	chr1:179857600-179865000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:179857600-179866600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:179857600-179867400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:179857600-179870000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:179857600-179871600	Weak transcription	HSMM	muscle
39	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
40	chr1:179857800-179861200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:179857800-179861600	Strong transcription	Osteobl	bone
42	chr1:179857800-179865000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:179858000-179866600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:179858200-179861200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:179858200-179861600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:179858200-179862000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:179858200-179864800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:179858200-179864800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:179858200-179865200	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:179858200-179865200	Strong transcription	Stomach Smooth Muscle	stomach

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