Variant report

Variant	rs36089963
Chromosome Location	chr3:23991026-23991027
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	chr3:23990941-23991555	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:23990907-23992320	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
4	MAFK	chr3:23991021-23991104	HepG2	liver:	n/a	n/a
5	IRF1	chr3:23990953-23992138	K562	blood:	n/a	chr3:23991957-23991971 chr3:23991960-23991973 chr3:23991959-23991979 chr3:23991961-23991971 chr3:23991963-23991977 chr3:23991960-23991973 chr3:23991955-23991976 chr3:23991955-23991972 chr3:23991960-23991974 chr3:23991965-23991978 chr3:23991957-23991974 chr3:23991960-23991971 chr3:23992018-23992035 chr3:23991960-23991972 chr3:23991959-23991973 chr3:23991960-23991973 chr3:23991961-23991975 chr3:23991959-23991970
6	FOXA2	chr3:23990924-23991860	HepG2	liver:	n/a	n/a
7	IRF1	chr3:23991011-23992343	K562	blood:	n/a	chr3:23991957-23991971 chr3:23991960-23991973 chr3:23991959-23991979 chr3:23991961-23991971 chr3:23991963-23991977 chr3:23991960-23991973 chr3:23991955-23991976 chr3:23991955-23991972 chr3:23991960-23991974 chr3:23991965-23991978 chr3:23991957-23991974 chr3:23991960-23991971 chr3:23992018-23992035 chr3:23991960-23991972 chr3:23991959-23991973 chr3:23991960-23991973 chr3:23991961-23991975 chr3:23991959-23991970
8	STAT1	chr3:23990981-23991915	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23988541..23991177-chr3:24537846..24539360,2	K562	blood:
3	chr3:23988335..23991846-chr3:24002543..24006084,3	K562	blood:
4	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
5	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000174738	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]
rs34058540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23987800-23991200	Enhancers	Fetal Heart	heart
2	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
3	chr3:23988200-23992200	Enhancers	Small Intestine	intestine
4	chr3:23988200-23992200	Enhancers	Stomach Mucosa	stomach
5	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
6	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
7	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:23988400-23991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:23988400-23991600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:23988400-23991800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
18	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
19	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:23988800-23991200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:23988800-23991200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:23989000-23991200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:23989000-23991200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:23989000-23991400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:23989000-23991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:23989000-23991400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:23989000-23991400	Weak transcription	Fetal Stomach	stomach
28	chr3:23989000-23991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:23989000-23991600	Enhancers	NHDF-Ad	bronchial
30	chr3:23989000-23991600	Enhancers	NHLF	lung
31	chr3:23989000-23992000	Enhancers	NHEK	skin
32	chr3:23989000-23992200	Enhancers	HepG2	liver
33	chr3:23989000-23992200	Enhancers	HMEC	breast
34	chr3:23989000-23993800	Enhancers	Liver	Liver
35	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:23989200-23991400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:23989200-23991400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:23989200-23991400	Enhancers	Hela-S3	cervix
41	chr3:23989200-23991600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:23989200-23991600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:23989200-23992200	Enhancers	A549	lung
44	chr3:23989200-23992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
47	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus

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