Variant report

Variant	rs12542490
Chromosome Location	chr8:19571745-19571746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10087146	0.85[CHB][hapmap]
rs10087676	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10095344	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10107740	0.86[CHB][hapmap]
rs10112753	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11992703	0.86[CHB][hapmap]
rs12114790	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12545833	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1552777	0.81[CHB][hapmap]
rs1845040	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28489490	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922081	0.86[CHB][hapmap]
rs4922082	0.86[CHB][hapmap]
rs4922091	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922092	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586859	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7002401	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7015372	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7016714	0.86[CHB][hapmap]
rs7016838	0.86[CHB][hapmap]
rs7840358	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7843312	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1021225	chr8:19554860-19586580	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19555000-19573200	Weak transcription	Pancreas	Pancrea
2	chr8:19555200-19573600	Weak transcription	Fetal Stomach	stomach
3	chr8:19558600-19573400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:19559200-19573400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:19559200-19573600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr8:19563200-19578200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:19567200-19572400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr8:19567400-19573400	Weak transcription	Right Ventricle	heart
9	chr8:19567600-19573200	Weak transcription	Right Atrium	heart
10	chr8:19568600-19574400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:19569000-19577600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:19569400-19575000	Weak transcription	Fetal Brain Male	brain
13	chr8:19569800-19575000	Weak transcription	Osteobl	bone
14	chr8:19570000-19573800	ZNF genes & repeats	A549	lung
15	chr8:19570400-19573200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr8:19570400-19573600	Strong transcription	Hela-S3	cervix
17	chr8:19570600-19572000	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr8:19570800-19571800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
19	chr8:19570800-19571800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr8:19570800-19571800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
21	chr8:19571000-19571800	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr8:19571000-19571800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr8:19571000-19571800	ZNF genes & repeats	Placenta	Placenta
24	chr8:19571000-19572000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr8:19571200-19576200	Weak transcription	Ovary	ovary
26	chr8:19571400-19571800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr8:19571400-19573200	Weak transcription	HUVEC	blood vessel
28	chr8:19571400-19573200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr8:19571400-19576800	Weak transcription	Aorta	Aorta
30	chr8:19571600-19572800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr8:19571600-19573200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:19571600-19573200	Weak transcription	Primary T cells from cord blood	blood
33	chr8:19571600-19573200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr8:19571600-19573400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:19571600-19573400	Weak transcription	Fetal Thymus	thymus
36	chr8:19571600-19573400	Weak transcription	Thymus	Thymus
37	chr8:19571600-19577200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links