Variant report

Variant	rs241666
Chromosome Location	chr3:60537755-60537756
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	chr3:60500352..60502884-chr3:60536251..60537952,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs151744	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1584339	0.91[EUR][1000 genomes]
rs1584340	0.91[EUR][1000 genomes]
rs171351	0.95[EUR][1000 genomes]
rs171352	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2121854	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2121856	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs241664	0.91[EUR][1000 genomes]
rs241673	0.95[EUR][1000 genomes]
rs241674	0.95[EUR][1000 genomes]
rs241676	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241677	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241678	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241679	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241680	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241682	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241683	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs241699	1.00[AFR][1000 genomes]
rs242185	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs242186	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs242188	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2594273	0.89[EUR][1000 genomes]
rs2682981	0.95[EUR][1000 genomes]
rs2682982	0.95[EUR][1000 genomes]
rs2734362	0.93[EUR][1000 genomes]
rs2856011	0.87[EUR][1000 genomes]
rs2856012	0.87[EUR][1000 genomes]
rs2856045	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1008235	chr3:60388277-60558331	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv460569	chr3:60388322-60558331	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590399	chr3:60388322-60558331	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2763271	chr3:60391557-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv999284	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1002453	chr3:60391557-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv948513	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1008661	chr3:60397271-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1010907	chr3:60425237-60557503	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1002978	chr3:60425237-60558331	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1014064	chr3:60448591-60558331	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1000393	chr3:60461450-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv876856	chr3:60472815-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv876857	chr3:60472815-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv590403	chr3:60484433-60558331	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv876859	chr3:60519576-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv876860	chr3:60531242-60557685	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv432422	chr3:60535731-60543215	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60533800-60541200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:60533800-60541200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:60533800-60541400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:60534000-60541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:60534200-60540600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:60534400-60541000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:60535200-60537800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:60536000-60540200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:60536200-60540600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:60536600-60540600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:60536800-60540600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:60537400-60538000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:60537600-60538400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:60537600-60538800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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