Variant report

Variant	rs57654087
Chromosome Location	chr1:174488961-174488962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1016465	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16847226	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56684280	0.92[AFR][1000 genomes]
rs57775442	1.00[AMR][1000 genomes]
rs58501155	0.85[AFR][1000 genomes]
rs59123040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59297292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59588705	1.00[AMR][1000 genomes]
rs59692051	1.00[AFR][1000 genomes]
rs60510552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73026418	0.92[AFR][1000 genomes]
rs73026420	0.92[AFR][1000 genomes]
rs73026424	0.92[AFR][1000 genomes]
rs73026442	0.85[AFR][1000 genomes]
rs73038687	0.85[AFR][1000 genomes]
rs73040875	0.92[AFR][1000 genomes]
rs73040884	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040885	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040887	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73042867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73042870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73042877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73042880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1003113	chr1:174367687-174499155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv535209	chr1:174367687-174499155	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
10	nsv1007667	chr1:174438778-174556953	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1009056	chr1:174457532-174549665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv548195	chr1:174469002-174519276	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174442200-174491800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174466800-174489800	Weak transcription	Left Ventricle	heart
3	chr1:174483800-174489800	Enhancers	Fetal Heart	heart
4	chr1:174486800-174493000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:174487800-174489600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:174487800-174489800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:174488200-174489200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:174488400-174489400	Enhancers	Fetal Brain Male	brain
9	chr1:174488600-174489400	Enhancers	Brain Hippocampus Middle	brain
10	chr1:174488600-174489600	Enhancers	Brain Angular Gyrus	brain
11	chr1:174488600-174499000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:174488800-174489200	Enhancers	Brain Anterior Caudate	brain
13	chr1:174488800-174489400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:174488800-174489400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:174488800-174489400	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:174488800-174489600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:174488800-174489600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:174488800-174489600	Enhancers	Fetal Brain Female	brain
19	chr1:174488800-174489800	Enhancers	Skeletal Muscle Male	skeletal muscle

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