Variant report

Variant	rs6850053
Chromosome Location	chr4:69920261-69920262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10012215	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10012240	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012607	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10021748	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030220	0.98[ASN][1000 genomes]
rs11725519	0.98[ASN][1000 genomes]
rs12501837	0.98[ASN][1000 genomes]
rs12509175	0.93[ASN][1000 genomes]
rs12648808	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12648830	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13102620	0.98[ASN][1000 genomes]
rs13108709	0.81[ASN][1000 genomes]
rs13116752	0.98[ASN][1000 genomes]
rs13127081	0.95[ASN][1000 genomes]
rs13140844	0.98[ASN][1000 genomes]
rs13145304	0.81[ASN][1000 genomes]
rs13147569	0.98[ASN][1000 genomes]
rs13147648	0.98[ASN][1000 genomes]
rs2292524	0.90[ASN][1000 genomes]
rs28775401	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28801471	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922514	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235108	0.96[ASN][1000 genomes]
rs4235111	0.98[ASN][1000 genomes]
rs4235112	0.98[ASN][1000 genomes]
rs4235113	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235114	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299665	0.98[ASN][1000 genomes]
rs4299666	0.98[ASN][1000 genomes]
rs4305590	0.96[ASN][1000 genomes]
rs4312824	0.98[ASN][1000 genomes]
rs4351079	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4353969	0.98[ASN][1000 genomes]
rs4365792	0.98[ASN][1000 genomes]
rs4377650	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4400060	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4400061	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4410590	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4412058	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4413468	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422474	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4440295	0.84[ASN][1000 genomes]
rs4446390	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4481286	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495114	0.98[ASN][1000 genomes]
rs4516791	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4518318	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4583828	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591680	0.98[ASN][1000 genomes]
rs4607293	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611997	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4618380	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694159	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4694160	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694588	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4694597	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694599	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694602	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694604	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694605	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694607	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694610	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694611	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694612	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55778959	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56879009	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57386454	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58496756	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60212682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60814050	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61612343	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6422321	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6422322	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600865	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6600867	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6600868	0.90[EUR][1000 genomes]
rs6827511	0.96[ASN][1000 genomes]
rs72851338	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72851348	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852416	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72852450	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7434389	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7435274	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7436912	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7438033	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438808	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7439419	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7441365	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7441736	0.96[ASN][1000 genomes]
rs7442394	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654272	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657426	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7658748	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7659987	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7660019	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7660021	0.84[ASN][1000 genomes]
rs7662632	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7666894	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674573	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674600	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7677996	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7679418	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7680156	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7687336	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7687692	0.84[ASN][1000 genomes]
rs7687725	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7692377	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7693166	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7698430	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9715099	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6850053	UGT2B7	cis	Skin Sun Exposed Lower leg	GTEx
rs6850053	UGT2B7	cis	lung	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69916200-69921200	Active TSS	HepG2	liver
2	chr4:69916800-69920400	Active TSS	Fetal Kidney	kidney
3	chr4:69917400-69922800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:69917600-69922800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:69917600-69923000	Weak transcription	GM12878-XiMat	blood
6	chr4:69917600-69923200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:69918000-69922000	Weak transcription	Liver	Liver
8	chr4:69918000-69922200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:69918200-69921600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:69918200-69921800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:69918200-69922800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:69918800-69922800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:69919400-69922800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:69919400-69923000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:69919400-69923200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:69919600-69922800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:69919600-69922800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:69919600-69923200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:69919600-69924000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:69920000-69920800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:69920200-69920600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:69920200-69920600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:69920200-69920600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:69920200-69920600	Enhancers	Pancreas	Pancrea
25	chr4:69920200-69920600	Enhancers	Small Intestine	intestine
26	chr4:69920200-69921200	Enhancers	Stomach Mucosa	stomach
27	chr4:69920200-69921200	Enhancers	HUVEC	blood vessel
28	chr4:69920200-69921400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links