Variant report

Variant	rs4539105
Chromosome Location	chr1:214669583-214669584
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	chr1:214659692..214662430-chr1:214669544..214671221,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10494980	0.84[CHB][hapmap]
rs10746445	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10746446	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864101	0.92[CHB][hapmap];0.90[CHD][hapmap];0.81[MKK][hapmap]
rs10864102	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11120321	0.87[CEU][hapmap]
rs11120329	0.92[CHB][hapmap]
rs11120330	0.92[CHB][hapmap]
rs11120334	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12068677	0.92[CHB][hapmap]
rs12128034	0.91[CHB][hapmap]
rs12726438	1.00[YRI][hapmap]
rs12743237	0.92[CHB][hapmap]
rs17023030	0.83[CHB][hapmap]
rs4130486	0.91[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4233305	0.87[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4233306	0.84[CHB][hapmap]
rs4233307	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253891	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4301608	0.87[CEU][hapmap]
rs4421564	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4451529	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4465172	0.87[CEU][hapmap];0.90[CHD][hapmap]
rs4655250	0.92[CHB][hapmap]
rs4655251	0.92[CHB][hapmap]
rs4655252	0.92[CHB][hapmap]
rs4655253	0.92[CHB][hapmap]
rs4655254	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs4655255	0.91[CHB][hapmap]
rs4655347	0.92[CHB][hapmap]
rs4655354	1.00[YRI][hapmap]
rs5020616	0.92[CHB][hapmap]
rs5020617	0.92[CHB][hapmap]
rs6540831	0.87[CEU][hapmap]
rs6540835	0.92[CHB][hapmap]
rs6540836	0.87[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6540839	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540840	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665797	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6668440	0.92[CHB][hapmap]
rs6682987	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7518513	0.90[CHB][hapmap]
rs7528679	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7528775	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7528800	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7535598	0.87[CEU][hapmap]
rs7537274	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7555415	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4539105	RPS6KC1	cis	cerebellum	SCAN
rs4539105	CENPF	cis	parietal	SCAN
rs4539105	PTPN14	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214646000-214672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:214654400-214677400	Weak transcription	Gastric	stomach
3	chr1:214663200-214673600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:214664800-214671800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:214664800-214672000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:214665000-214669600	Weak transcription	Spleen	Spleen
7	chr1:214665400-214676600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:214665400-214705400	Weak transcription	Right Ventricle	heart
9	chr1:214665600-214670200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:214666600-214669600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:214666600-214671600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:214666600-214672400	Weak transcription	Ovary	ovary
13	chr1:214666600-214672400	Enhancers	Osteobl	bone
14	chr1:214666600-214673800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:214666600-214675200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:214666600-214677600	Weak transcription	Pancreas	Pancrea
17	chr1:214666800-214670600	Enhancers	NHEK	skin
18	chr1:214666800-214671200	Weak transcription	Adipose Nuclei	Adipose
19	chr1:214667400-214670800	Enhancers	HMEC	breast
20	chr1:214667600-214670000	Enhancers	HSMM	muscle
21	chr1:214667800-214670000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:214667800-214670000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:214668000-214673200	Weak transcription	Placenta	Placenta
24	chr1:214668200-214671000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:214668400-214669600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:214668400-214669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:214668400-214669600	Weak transcription	Psoas Muscle	Psoas
28	chr1:214668400-214670000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:214668400-214670000	Enhancers	A549	lung
30	chr1:214668400-214673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:214668400-214673200	Weak transcription	NHLF	lung
32	chr1:214668400-214673600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:214668400-214673600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:214668400-214677600	Weak transcription	Left Ventricle	heart
35	chr1:214668400-214678600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:214668400-214680400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:214668600-214669600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:214668600-214669600	Weak transcription	HSMMtube	muscle
39	chr1:214668600-214670400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:214668600-214670600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:214668600-214671000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:214668600-214673600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:214668600-214677400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:214668800-214674200	Weak transcription	Fetal Heart	heart
45	chr1:214669200-214669800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:214669200-214669800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:214669200-214669800	Enhancers	Hela-S3	cervix
48	chr1:214669200-214670000	Enhancers	HUVEC	blood vessel
49	chr1:214669200-214670600	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:214669200-214671200	Enhancers	Colon Smooth Muscle	Colon

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