Variant report

Variant	rs7545544
Chromosome Location	chr1:77998764-77998765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77996828..77998774-chr1:78147470..78149282,2	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013399	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782654	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873949	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873950	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10873951	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11162362	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162363	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162364	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162365	0.90[ASN][1000 genomes]
rs11162369	0.83[ASN][1000 genomes]
rs11162372	0.81[ASN][1000 genomes]
rs12071212	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074409	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12095064	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142671	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.90[ASN][1000 genomes]
rs12724560	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565850	0.93[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565851	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs1565852	0.86[ASN][1000 genomes]
rs1962523	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1976334	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029768	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.97[ASN][1000 genomes]
rs2133202	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2172727	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2647486	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647487	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278854	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803136	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2803168	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773766	0.89[ASN][1000 genomes]
rs3509	0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs371076	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs3738079	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767030	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs3767032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767033	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245658	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4589153	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600093	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949657	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949658	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949659	0.85[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949807	0.95[ASN][1000 genomes]
rs4949808	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949809	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949811	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs4949813	0.91[ASN][1000 genomes]
rs4949814	0.81[YRI][hapmap]
rs4949816	0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6603952	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6603953	0.91[ASN][1000 genomes]
rs6603955	0.90[ASN][1000 genomes]
rs6667519	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6667803	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675743	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6692369	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695989	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696083	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728741	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7513619	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519476	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524147	0.94[ASN][1000 genomes]
rs7524866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7531286	0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7546365	0.80[ASW][hapmap]
rs7551211	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551729	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552291	0.83[MKK][hapmap]
rs872342	0.83[CHD][hapmap]
rs962388	0.91[ASN][1000 genomes]
rs9787153	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3382945	chr1:77996914-77999212	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7545544	AK5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77980800-77999400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:77981800-77999200	Weak transcription	NHLF	lung
3	chr1:77981800-77999400	Weak transcription	HSMMtube	muscle
4	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:77985200-77999400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:77985400-77999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:77988400-77999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:77988600-77999400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:77992000-77999000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:77992000-77999200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:77992000-77999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:77992000-77999200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:77992200-77999200	Weak transcription	Primary T cells from cord blood	blood
14	chr1:77992200-77999200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:77993400-77999400	Weak transcription	HSMM	muscle
16	chr1:77996600-77999600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:77996600-77999600	Weak transcription	HMEC	breast
18	chr1:77996800-77999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:77996800-77999800	Weak transcription	NHEK	skin
20	chr1:77996800-78001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:77998200-77999400	Enhancers	Brain Anterior Caudate	brain
23	chr1:77998200-78000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:77998200-78000000	Enhancers	NHDF-Ad	bronchial
25	chr1:77998200-78000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:77998200-78000200	Enhancers	Brain Angular Gyrus	brain
27	chr1:77998200-78000400	Enhancers	Brain Hippocampus Middle	brain
28	chr1:77998200-78000600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:77998200-78005000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:77998400-77999600	Enhancers	Fetal Muscle Leg	muscle
31	chr1:77998400-77999600	Enhancers	Osteobl	bone
32	chr1:77998400-78000600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:77998600-77999000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:77998600-77999200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:77998600-77999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:77998600-77999600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:77998600-77999600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links