Variant report

Variant	rs2542302
Chromosome Location	chr19:40491969-40491970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40491586..40493353-chr19:40595299..40596901,2	MCF-7	breast:
2	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:
3	chr19:40491047..40493453-chr19:40495126..40496667,2	K562	blood:
4	chr19:40490913..40493300-chr19:40497189..40499591,2	K562	blood:
5	chr19:40491800..40493887-chr19:40495833..40498689,2	K562	blood:

Variant related genes	Relation type
ENSG00000269749	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000197782	Chromatin interaction
ENSG00000221233	Chromatin interaction
ENSG00000269296	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10403646	0.90[AMR][1000 genomes]
rs10410695	1.00[EUR][1000 genomes]
rs10418448	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs10427117	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs234297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234307	1.00[EUR][1000 genomes]
rs234312	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234316	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs234319	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs234321	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs234322	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs234327	0.89[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234339	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs234342	1.00[EUR][1000 genomes]
rs234359	0.84[YRI][hapmap]
rs28661993	1.00[EUR][1000 genomes]
rs28776318	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28832070	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337795	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245930	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250945	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257627	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258111	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258718	0.90[AMR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930679	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2542302	ZNF780A	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40477800-40501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40478600-40501800	Weak transcription	Right Atrium	heart
3	chr19:40485800-40494600	ZNF genes & repeats	A549	lung
4	chr19:40486800-40492800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:40487200-40499600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:40487600-40492200	Weak transcription	Fetal Brain Male	brain
7	chr19:40487600-40501800	Weak transcription	Right Ventricle	heart
8	chr19:40488200-40492400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:40488200-40497000	Weak transcription	Pancreas	Pancrea
10	chr19:40488200-40497400	Weak transcription	Gastric	stomach
11	chr19:40488200-40499600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:40488200-40501800	Weak transcription	Esophagus	oesophagus
13	chr19:40488400-40492600	Weak transcription	Brain Angular Gyrus	brain
14	chr19:40488400-40501800	Weak transcription	Left Ventricle	heart
15	chr19:40488800-40501800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:40489000-40501600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:40489400-40494800	Weak transcription	Placenta	Placenta
18	chr19:40489600-40500200	Weak transcription	Fetal Kidney	kidney
19	chr19:40490000-40492400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:40490000-40492400	Weak transcription	HUVEC	blood vessel
21	chr19:40490000-40492600	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:40490000-40492600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:40490000-40493200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:40490000-40497200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:40490200-40492200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:40490200-40492400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:40490200-40492400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:40490200-40492400	Weak transcription	Psoas Muscle	Psoas
29	chr19:40490200-40499600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:40490200-40499600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:40490200-40499800	Weak transcription	Lung	lung
32	chr19:40490200-40501600	Weak transcription	HSMM	muscle
33	chr19:40490200-40501600	Weak transcription	Osteobl	bone
34	chr19:40490200-40501800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:40490200-40501800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:40490200-40502400	Weak transcription	Aorta	Aorta
37	chr19:40490400-40499600	Weak transcription	Fetal Thymus	thymus
38	chr19:40490400-40501800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:40491000-40502200	Weak transcription	Ovary	ovary

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