Variant report

Variant	rs60164080
Chromosome Location	chr1:223986844-223986845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1003061	0.86[ASN][1000 genomes]
rs1153927	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153929	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153930	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153933	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153934	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153936	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153937	0.95[EUR][1000 genomes]
rs1153938	0.95[EUR][1000 genomes]
rs1153943	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1153947	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153949	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153971	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153973	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222120	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1222121	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1222124	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222128	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222146	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222156	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1621129	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629850	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16842270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842294	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16842321	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1981171	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982610	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1982612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1982613	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242188	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370163	0.87[EUR][1000 genomes]
rs28370164	0.87[EUR][1000 genomes]
rs28370167	0.87[EUR][1000 genomes]
rs28370172	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738370	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653457	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56329085	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56918361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59104475	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59196624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60131749	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60739082	0.85[ASN][1000 genomes]
rs6604726	0.83[ASN][1000 genomes]
rs6661816	0.87[ASN][1000 genomes]
rs6675712	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6687003	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6694214	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749554	0.89[EUR][1000 genomes]
rs72749569	0.92[EUR][1000 genomes]
rs72749588	0.89[ASN][1000 genomes]
rs737066	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs750873	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7536779	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs898878	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	esv3358086	chr1:223986455-223987014	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a
10	esv3335454	chr1:223986475-223986984	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
4	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
8	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:223969800-223995200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:223970000-223995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:223970600-223990400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:223972800-223995200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:223973200-223996000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:223974000-223995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:223975000-223989800	Strong transcription	Liver	Liver
17	chr1:223975800-223995200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:223976800-224003000	Weak transcription	Fetal Heart	heart
19	chr1:223977600-223993400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:223978200-223995000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:223978400-223994200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:223978400-223994800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:223978800-223997200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:223979000-223995600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:223979000-224000800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:223979200-223995800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:223979200-224002200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:223979400-224002600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:223979600-223991400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:223979600-223992200	Strong transcription	Placenta	Placenta
31	chr1:223979600-223992400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:223979600-223994000	Strong transcription	NH-A	brain
33	chr1:223979600-223994600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:223979600-223994800	Strong transcription	Primary B cells from cord blood	blood
35	chr1:223979600-224002400	Strong transcription	Dnd41	blood
36	chr1:223979800-223996000	Strong transcription	Primary T cells from cord blood	blood
37	chr1:223979800-223997000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:223981000-223990000	Strong transcription	HSMM	muscle
39	chr1:223981200-223989200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:223981200-223995800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:223981800-224002600	Weak transcription	Stomach Mucosa	stomach
42	chr1:223982400-223997800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:223982600-223994600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:223982600-223997600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:223982800-223988400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:223982800-223988800	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:223982800-223991000	Strong transcription	Fetal Brain Female	brain
48	chr1:223982800-223994000	Strong transcription	Left Ventricle	heart
49	chr1:223982800-223994600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:223982800-223995200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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