Variant report

Variant	rs34058540
Chromosome Location	chr3:23995658-23995659
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	chr3:23994885-23996788	HepG2	liver:	n/a	n/a
2	EP300	chr3:23994685-23995779	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:23995481-23995701	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10084748	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[ASN][1000 genomes]
rs11129128	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13321439	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13321440	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533141	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1567579	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34866549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35755171	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[ASN][1000 genomes]
rs6776568	1.00[ASN][1000 genomes]
rs6778577	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790140	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71324126	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72627094	0.83[AMR][1000 genomes]
rs73150266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[ASN][1000 genomes]
rs7611018	1.00[ASN][1000 genomes]
rs954748	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[ASN][1000 genomes]
rs9812870	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9817923	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9853954	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	1.00[ASN][1000 genomes]
rs9863176	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[ASN][1000 genomes]
rs9883834	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
2	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
7	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
12	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
16	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
17	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
24	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
25	chr3:23989800-23996000	Weak transcription	Osteobl	bone
26	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
28	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:23990400-23996200	Weak transcription	Placenta	Placenta
30	chr3:23990400-23997600	Weak transcription	NH-A	brain
31	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:23990800-23995800	Enhancers	Primary B cells from cord blood	blood
33	chr3:23991000-23996000	Enhancers	Primary B cells from peripheral blood	blood
34	chr3:23991000-23996400	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:23991400-23996000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:23991600-23996000	Enhancers	Colon Smooth Muscle	Colon
37	chr3:23991600-23996200	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:23991800-23996200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:23991800-23996200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:23991800-23996400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:23991800-23999600	Weak transcription	HSMMtube	muscle
42	chr3:23992000-23996000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:23992000-23996000	Weak transcription	Hela-S3	cervix
44	chr3:23992000-23996000	Weak transcription	HSMM	muscle
45	chr3:23992000-23996200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:23992000-23996400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:23992000-24000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:23992000-24001600	Weak transcription	Fetal Stomach	stomach
49	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
50	chr3:23992200-23996000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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