Variant report

Variant	rs7143560
Chromosome Location	chr14:56695047-56695048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10132757	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152004	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1023120	0.84[CHD][hapmap]
rs1028973	0.84[CHD][hapmap]
rs1152464	0.92[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1152466	0.84[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1152478	0.81[CEU][hapmap]
rs1188693	0.87[GIH][hapmap]
rs12589133	0.84[ASN][1000 genomes]
rs12589933	0.92[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1382974	0.94[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1382977	0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17091062	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs17091112	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs17091123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17091196	0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs17761563	0.84[MEX][hapmap]
rs2228708	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2297610	0.84[CHB][hapmap]
rs242413	0.84[TSI][hapmap]
rs242581	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs242582	0.85[ASN][1000 genomes]
rs28662163	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs385141	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs3898605	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4636823	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs58116791	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61311029	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6573085	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6573086	0.87[ASW][hapmap]
rs7141484	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7141949	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7152487	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7161103	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7161274	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs754314	0.90[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8009804	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8011852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8014574	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][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	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7143560	PTGER2	cis	cerebellum	SCAN
rs7143560	ARID4A	cis	cerebellum	SCAN
rs7143560	PSMC6	cis	cerebellum	SCAN
rs7143560	C14orf166	cis	cerebellum	SCAN
rs7143560	ERO1L	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56682200-56699200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr14:56686800-56702000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr14:56688000-56707800	Weak transcription	Spleen	Spleen
4	chr14:56688800-56695400	Weak transcription	Fetal Thymus	thymus
5	chr14:56689600-56695200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:56689600-56695400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:56689600-56699200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr14:56689600-56710000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:56689800-56715800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:56691800-56696000	Strong transcription	Thymus	Thymus
11	chr14:56692000-56696200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:56692400-56703000	Weak transcription	Aorta	Aorta
13	chr14:56692400-56710000	Weak transcription	Fetal Stomach	stomach
14	chr14:56692600-56701400	Weak transcription	Ovary	ovary
15	chr14:56692600-56703200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:56692800-56699200	Weak transcription	Stomach Mucosa	stomach
17	chr14:56693000-56704000	Weak transcription	Primary T cells from cord blood	blood
18	chr14:56693200-56703000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:56693200-56724400	Weak transcription	Gastric	stomach
20	chr14:56693600-56695200	ZNF genes & repeats	Dnd41	blood
21	chr14:56694000-56701600	Weak transcription	Pancreas	Pancrea
22	chr14:56694000-56723000	Weak transcription	Lung	lung
23	chr14:56694200-56695800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr14:56694800-56696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr14:56695000-56696800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links