Variant report

Variant	rs58390229
Chromosome Location	chr9:100369325-100369326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:100369299-100370235	K562	blood:	n/a	n/a
2	POLR2A	chr9:100360719-100370063	K562	blood:	n/a	n/a

Variant related genes	Relation type
TSTD2	TF binding region

Extended variants
information (count: 175 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs1034098	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1034099	0.97[ASN][1000 genomes]
rs10512254	0.81[ASN][1000 genomes]
rs1116208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1126122	0.93[ASN][1000 genomes]
rs12345701	0.90[ASN][1000 genomes]
rs12349801	0.85[ASN][1000 genomes]
rs14066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1411344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1543636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16922319	0.95[ASN][1000 genomes]
rs16923041	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16923112	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1928641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1928642	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2282066	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2282067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2297155	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2297156	0.87[AFR][1000 genomes]
rs2297157	0.81[ASN][1000 genomes]
rs2297158	0.87[AFR][1000 genomes]
rs2297159	0.87[AFR][1000 genomes]
rs2297160	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2401635	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28403588	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28403589	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3176623	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176624	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176626	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176628	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176629	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176634	0.82[AFR][1000 genomes]
rs3176637	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176638	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176642	0.81[ASN][1000 genomes]
rs3176644	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176645	0.81[ASN][1000 genomes]
rs3176651	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176654	0.81[ASN][1000 genomes]
rs3176659	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176665	0.81[ASN][1000 genomes]
rs3176668	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176669	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176670	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176673	0.81[ASN][1000 genomes]
rs3176675	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176682	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176685	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176688	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176694	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176698	0.81[ASN][1000 genomes]
rs3176700	0.81[ASN][1000 genomes]
rs3176703	0.81[ASN][1000 genomes]
rs3176708	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176714	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176720	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176721	0.81[ASN][1000 genomes]
rs3176723	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176724	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176726	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176728	0.81[ASN][1000 genomes]
rs3176734	0.81[ASN][1000 genomes]
rs3176735	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176736	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176739	0.81[ASN][1000 genomes]
rs3176740	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176744	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176746	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176747	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3176751	0.81[ASN][1000 genomes]
rs3176752	0.81[ASN][1000 genomes]
rs3176758	0.81[ASN][1000 genomes]
rs3176759	0.81[ASN][1000 genomes]
rs3750368	0.97[ASN][1000 genomes]
rs3750369	0.97[ASN][1000 genomes]
rs3750370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3763606	0.93[ASN][1000 genomes]
rs3802472	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3802473	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3802474	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3824494	0.97[ASN][1000 genomes]
rs3897841	0.95[ASN][1000 genomes]
rs41274252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55966848	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56052819	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56060429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56164437	0.95[ASN][1000 genomes]
rs56200116	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs57188235	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57598118	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs57940370	0.81[ASN][1000 genomes]
rs58146508	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58387091	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58637778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58878935	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58933803	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59205756	0.81[ASN][1000 genomes]
rs59354722	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59478543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59662386	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59775587	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59791764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59992945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60026475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60028882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60055057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60104153	0.88[AMR][1000 genomes]
rs60359353	0.93[ASN][1000 genomes]
rs60463150	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs60596698	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60653177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60821994	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs60822454	0.87[ASN][1000 genomes]
rs61152667	0.97[ASN][1000 genomes]
rs61208411	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61221847	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61276200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61440789	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61445476	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61739366	0.82[AFR][1000 genomes]
rs6478304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6478305	0.84[AFR][1000 genomes]
rs7018546	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7025403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7036604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7045160	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7049183	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7341850	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498323	0.80[AFR][1000 genomes]
rs73498324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498332	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498338	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498362	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73498377	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73498380	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73498381	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73498394	0.81[ASN][1000 genomes]
rs73500325	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500326	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500328	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500393	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500395	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500396	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500397	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500398	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73500400	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73502204	0.81[ASN][1000 genomes]
rs73551090	0.82[AFR][1000 genomes]
rs73552509	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73552512	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73552520	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73554629	0.97[ASN][1000 genomes]
rs73554631	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73554641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73554646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73554650	0.83[AFR][1000 genomes]
rs73554652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7850986	0.87[AFR][1000 genomes]
rs7856316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7857174	0.83[AFR][1000 genomes]
rs7859684	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7859979	0.83[AFR][1000 genomes]
rs7862356	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7866961	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7867046	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7869683	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9539	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9777684	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:100361000-100381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:100361400-100370000	Strong transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:100361600-100369400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:100361600-100369800	Strong transcription	Dnd41	blood
6	chr9:100361600-100370200	Strong transcription	Brain Hippocampus Middle	brain
7	chr9:100361600-100371000	Strong transcription	Brain Inferior Temporal Lobe	brain
8	chr9:100361600-100371200	Strong transcription	Liver	Liver
9	chr9:100361600-100371400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:100361600-100371600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:100361600-100375800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:100361800-100369400	Strong transcription	Brain Cingulate Gyrus	brain
13	chr9:100361800-100369800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:100361800-100370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:100361800-100371200	Strong transcription	Placenta	Placenta
16	chr9:100361800-100371200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr9:100361800-100371400	Strong transcription	Primary B cells from cord blood	blood
18	chr9:100361800-100371400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:100361800-100371400	Strong transcription	Fetal Stomach	stomach
20	chr9:100361800-100371400	Strong transcription	Lung	lung
21	chr9:100361800-100374000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:100361800-100374400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:100361800-100375800	Strong transcription	Primary T cells from cord blood	blood
24	chr9:100361800-100376000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:100361800-100376000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr9:100361800-100376000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:100361800-100376000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:100361800-100383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:100361800-100389000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr9:100362000-100369800	Strong transcription	Fetal Lung	lung
32	chr9:100362000-100370000	Strong transcription	Fetal Intestine Large	intestine
33	chr9:100362200-100373800	Weak transcription	Fetal Brain Male	brain
34	chr9:100362200-100379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:100362400-100369800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:100362400-100369800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:100362400-100371600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:100362400-100376400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:100362400-100376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:100362600-100371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:100362600-100371600	Strong transcription	Fetal Brain Female	brain
42	chr9:100362600-100376000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:100362800-100370000	Strong transcription	Colon Smooth Muscle	Colon
44	chr9:100362800-100370600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:100363000-100369600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr9:100363000-100371200	Strong transcription	Thymus	Thymus
47	chr9:100363000-100371400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:100363000-100374400	Strong transcription	Brain Germinal Matrix	brain
49	chr9:100363000-100394600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr9:100363200-100370200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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