Variant report

Variant	rs1039009
Chromosome Location	chr1:247080458-247080459
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247074467..247081092-chr1:247083777..247087568,7	K562	blood:
2	chr1:247071509..247075202-chr1:247075216..247082853,9	K562	blood:
3	chr1:247079113..247081115-chr1:247093616..247096368,2	K562	blood:
4	chr1:247077579..247081444-chr1:247089361..247091702,5	K562	blood:

Variant related genes	Relation type
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1039010	1.00[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11579381	0.86[JPT][hapmap]
rs11585741	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1472275	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1612610	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1613209	0.93[EUR][1000 genomes]
rs1619941	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1691240	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1691241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1691242	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1691245	0.82[MEX][hapmap]
rs1691246	0.82[MEX][hapmap]
rs1691252	1.00[ASW][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1691254	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1691255	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779964	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1779968	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779969	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779985	0.82[MEX][hapmap]
rs2172796	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642975	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2642977	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642990	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2642991	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2800214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800215	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800219	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800220	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2800221	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818888	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971278	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7542895	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs768197	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs903461	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9729306	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9729316	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS 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	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1039009	ZNF124	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:247043800-247082000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:247045400-247082600	Strong transcription	Dnd41	blood
6	chr1:247045800-247082400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:247045800-247083400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:247046000-247081400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:247046000-247082000	Strong transcription	Fetal Thymus	thymus
10	chr1:247046000-247082800	Strong transcription	Hela-S3	cervix
11	chr1:247046200-247081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:247046200-247081400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:247046200-247081400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:247055400-247089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:247056000-247084800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:247057800-247085400	Weak transcription	Pancreas	Pancrea
17	chr1:247061200-247093000	Weak transcription	Fetal Brain Male	brain
18	chr1:247061400-247082200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:247063800-247081000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:247065600-247088800	Weak transcription	Small Intestine	intestine
21	chr1:247068200-247081800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:247068400-247082000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:247069400-247087000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:247069600-247082400	Weak transcription	Right Ventricle	heart
25	chr1:247069600-247093400	Weak transcription	Colonic Mucosa	Colon
26	chr1:247069600-247093400	Weak transcription	Esophagus	oesophagus
27	chr1:247069800-247082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:247069800-247087000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:247069800-247087000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:247069800-247093800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:247070000-247093600	Weak transcription	Aorta	Aorta
32	chr1:247070400-247087000	Weak transcription	Lung	lung
33	chr1:247070800-247092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:247071000-247093400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:247071200-247082800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:247071200-247087000	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:247071400-247082000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:247071800-247081400	Strong transcription	Liver	Liver
39	chr1:247072000-247082800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:247072200-247081400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:247072200-247088800	Weak transcription	Fetal Intestine Small	intestine
42	chr1:247072600-247080800	Strong transcription	Placenta	Placenta
43	chr1:247072600-247081000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:247072600-247081200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:247072600-247081200	Strong transcription	Adipose Nuclei	Adipose
46	chr1:247072600-247081400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:247072800-247080800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:247072800-247081000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:247072800-247081000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:247072800-247081400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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