Variant report

Variant	rs2764909
Chromosome Location	chr1:59406853-59406854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59405293..59407465-chr1:59409123..59412417,3	K562	blood:
2	chr1:59248910..59251256-chr1:59406675..59408781,2	K562	blood:
3	chr1:59246952..59251848-chr1:59405165..59409884,6	K562	blood:
4	chr1:59401291..59404305-chr1:59406315..59409384,3	MCF-7	breast:
5	chr1:59403568..59405263-chr1:59405379..59408693,3	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12071047	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089816	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093908	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096897	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs17118423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118441	0.91[EUR][1000 genomes]
rs1886744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011623	0.89[MEX][hapmap]
rs2477743	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716161	0.82[ASW][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs2764908	0.82[ASW][hapmap];0.89[MEX][hapmap]
rs2999129	0.82[ASW][hapmap];0.89[MEX][hapmap]
rs35393496	0.89[EUR][1000 genomes]
rs55675910	0.89[EUR][1000 genomes]
rs55834295	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55872264	0.89[EUR][1000 genomes]
rs56175432	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56219110	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251271	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349902	0.89[EUR][1000 genomes]
rs6681035	0.80[GIH][hapmap];0.81[MEX][hapmap]
rs72678885	0.89[EUR][1000 genomes]
rs72678896	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678899	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678900	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678901	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680106	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680107	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680109	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680113	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2764909	NFIA	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
2	chr1:59399000-59407000	Weak transcription	Lung	lung
3	chr1:59399200-59407200	Weak transcription	Colonic Mucosa	Colon
4	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:59401600-59407000	Weak transcription	Gastric	stomach
6	chr1:59402600-59408400	Weak transcription	A549	lung
7	chr1:59403200-59408000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:59403200-59408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:59403200-59408200	Weak transcription	NHEK	skin
10	chr1:59403400-59408000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:59403400-59408200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:59403400-59408200	Weak transcription	HMEC	breast
13	chr1:59404400-59407200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:59405000-59407200	Enhancers	Primary T cells from cord blood	blood
15	chr1:59405000-59407200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:59405200-59407000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:59405200-59407200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:59405200-59407200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:59405400-59410800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:59405600-59407000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:59405600-59407000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr1:59405600-59407000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:59405600-59407200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:59405800-59407000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:59405800-59407200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:59406000-59407000	Weak transcription	Pancreas	Pancrea
27	chr1:59406200-59407800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:59406600-59408200	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:59406600-59408600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:59406600-59409200	Enhancers	Primary B cells from cord blood	blood
31	chr1:59406600-59410600	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:59406600-59410800	Enhancers	Fetal Thymus	thymus
33	chr1:59406800-59407000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:59406800-59407000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:59406800-59407000	Bivalent Enhancer	HepG2	liver
36	chr1:59406800-59407400	Flanking Active TSS	Dnd41	blood
37	chr1:59406800-59407800	Enhancers	Esophagus	oesophagus
38	chr1:59406800-59408400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
39	chr1:59406800-59408600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:59406800-59409000	Enhancers	Adipose Nuclei	Adipose

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