Variant report

Variant	rs9425853
Chromosome Location	chr1:180021050-180021051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179851411..179853011-chr1:180019045..180021728,2	MCF-7	breast:
2	chr1:179998356..180000949-chr1:180019994..180021642,2	K562	blood:
3	chr1:180010544..180012138-chr1:180019393..180021137,2	K562	blood:
4	chr1:180012630..180014181-chr1:180020336..180022043,2	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10798729	0.80[JPT][hapmap]
rs10913916	0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10913917	0.81[JPT][hapmap]
rs10913918	0.84[CEU][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12075450	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12091685	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs16855164	0.99[ASN][1000 genomes]
rs1981314	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2319676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2319677	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2319773	0.89[ASN][1000 genomes]
rs2477106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477107	0.89[ASN][1000 genomes]
rs2477109	0.87[ASN][1000 genomes]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2477113	0.85[ASN][1000 genomes]
rs2477115	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2477117	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2483622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501614	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501615	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2501618	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501619	0.84[ASN][1000 genomes]
rs2501621	0.93[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2762859	0.81[JPT][hapmap]
rs3123521	0.90[ASN][1000 genomes]
rs3767201	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3818999	0.81[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.93[JPT][hapmap]
rs4147170	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4256775	0.93[JPT][hapmap]
rs4263962	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4379644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4622030	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4651055	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652461	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652464	0.89[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.81[JPT][hapmap]
rs510209	0.81[JPT][hapmap]
rs552743	0.84[CEU][hapmap]
rs55953436	0.87[EUR][1000 genomes]
rs55971224	0.86[EUR][1000 genomes]
rs6425602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425603	0.93[JPT][hapmap]
rs6425606	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6425607	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6659911	0.95[ASN][1000 genomes]
rs6660984	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6676989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682558	0.88[CEU][hapmap]
rs6692394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7521895	0.80[CHB][hapmap]
rs7521948	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547954	0.81[EUR][1000 genomes]
rs9286932	0.93[JPT][hapmap]
rs9425849	0.93[JPT][hapmap]
rs9425852	0.98[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.93[ASN][1000 genomes]
rs9425858	0.88[ASN][1000 genomes]
rs9425859	0.80[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv3755	chr1:179998860-180043554	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1000698	chr1:179999669-180042521	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:179980400-180027400	Strong transcription	Dnd41	blood
5	chr1:179981000-180027200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:179985600-180024800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:179989800-180034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:179990000-180025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:179990200-180025400	Weak transcription	Pancreas	Pancrea
12	chr1:179992400-180031400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:179992400-180032200	Weak transcription	Esophagus	oesophagus
14	chr1:180000200-180029200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:180000600-180026600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:180000600-180039800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:180002400-180027000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:180002800-180027200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:180004200-180025600	Weak transcription	Lung	lung
22	chr1:180005800-180022800	Weak transcription	Small Intestine	intestine
23	chr1:180008800-180028200	Strong transcription	Fetal Intestine Large	intestine
24	chr1:180009000-180027800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:180009000-180041200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:180009000-180069600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:180009200-180024800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:180009200-180026600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:180009200-180027200	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:180009200-180051800	Strong transcription	Fetal Thymus	thymus
31	chr1:180009200-180070000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:180009600-180021800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:180010000-180024600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:180010000-180024600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:180010000-180024600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:180010000-180024600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:180010200-180023000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:180010200-180026000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:180010200-180026200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:180010200-180026600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:180010200-180029000	Strong transcription	Primary B cells from cord blood	blood
42	chr1:180010200-180040400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:180010200-180052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:180010600-180024600	Strong transcription	Primary T cells from cord blood	blood
45	chr1:180010600-180024800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:180010600-180051800	Strong transcription	Liver	Liver
47	chr1:180010800-180023600	Strong transcription	HepG2	liver
48	chr1:180010800-180024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:180010800-180024400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:180010800-180028600	Strong transcription	Adipose Nuclei	Adipose

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