Variant report

Variant	rs557104
Chromosome Location	chr6:165769426-165769427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs13202475	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13205683	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1706115	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706117	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1706118	0.82[ASN][1000 genomes]
rs1706121	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1706123	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1740807	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1740811	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1740812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479290	1.00[ASN][1000 genomes]
rs480219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480275	1.00[ASN][1000 genomes]
rs482128	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485667	0.99[ASN][1000 genomes]
rs486002	0.97[ASN][1000 genomes]
rs487489	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489431	1.00[ASN][1000 genomes]
rs491253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493931	0.91[ASN][1000 genomes]
rs495725	0.91[ASN][1000 genomes]
rs499235	1.00[ASN][1000 genomes]
rs500017	0.99[ASN][1000 genomes]
rs5003411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501712	0.86[ASN][1000 genomes]
rs502012	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504371	0.85[ASN][1000 genomes]
rs504498	0.90[ASN][1000 genomes]
rs507362	0.99[ASN][1000 genomes]
rs509909	1.00[ASN][1000 genomes]
rs512584	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521211	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522248	0.91[ASN][1000 genomes]
rs522390	0.91[ASN][1000 genomes]
rs523056	0.91[ASN][1000 genomes]
rs524122	0.91[ASN][1000 genomes]
rs525984	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528319	0.90[ASN][1000 genomes]
rs528361	0.90[ASN][1000 genomes]
rs528450	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529165	0.90[ASN][1000 genomes]
rs529247	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531974	0.90[ASN][1000 genomes]
rs532173	0.90[ASN][1000 genomes]
rs533040	0.90[ASN][1000 genomes]
rs534925	0.89[ASN][1000 genomes]
rs536502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536555	1.00[ASN][1000 genomes]
rs537436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547832	0.90[ASN][1000 genomes]
rs547889	0.90[ASN][1000 genomes]
rs550108	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550811	0.90[ASN][1000 genomes]
rs551504	0.90[ASN][1000 genomes]
rs554575	0.96[ASN][1000 genomes]
rs556752	0.90[ASN][1000 genomes]
rs557916	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564788	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571366	0.91[ASN][1000 genomes]
rs572280	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574295	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs575092	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575669	0.97[ASN][1000 genomes]
rs579312	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590993	0.90[ASN][1000 genomes]
rs592768	0.91[ASN][1000 genomes]
rs617910	0.84[ASN][1000 genomes]
rs619736	0.91[ASN][1000 genomes]
rs622800	0.91[ASN][1000 genomes]
rs635179	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs637343	0.90[ASN][1000 genomes]
rs637735	0.90[ASN][1000 genomes]
rs688805	0.92[ASN][1000 genomes]
rs7766706	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860401	0.91[ASN][1000 genomes]
rs9459398	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432982	chr6:165528589-165835589	Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv605245	chr6:165542686-165845903	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1031648	chr6:165544569-165841029	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv432983	chr6:165554403-165851585	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3417270	chr6:165682773-166023032	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv886928	chr6:165722345-166197889	Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165744800-165801200	Weak transcription	Hela-S3	cervix
2	chr6:165745200-165770000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:165745600-165802800	Weak transcription	Fetal Heart	heart
4	chr6:165747400-165802600	Weak transcription	HSMMtube	muscle
5	chr6:165747600-165853000	Weak transcription	A549	lung
6	chr6:165749200-165769800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:165749800-165775000	Weak transcription	Fetal Lung	lung
8	chr6:165763800-165770800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:165763800-165771200	Weak transcription	Brain Angular Gyrus	brain
10	chr6:165763800-165775800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:165763800-165789600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:165763800-165797000	Weak transcription	Right Ventricle	heart
13	chr6:165763800-165797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:165764200-165769600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:165764200-165775000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:165764400-165813400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:165766600-165770400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:165766600-165776000	Weak transcription	Psoas Muscle	Psoas
19	chr6:165768200-165772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:165768800-165771600	Strong transcription	HSMM	muscle
21	chr6:165769000-165769800	Strong transcription	Left Ventricle	heart
22	chr6:165769000-165769800	Strong transcription	Ovary	ovary
23	chr6:165769400-165769800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links