Variant report

Variant	rs238670
Chromosome Location	chr20:23488710-23488711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23486686..23489080-chr20:23489324..23491431,2	MCF-7	breast:
2	chr20:23482103..23484253-chr20:23488282..23490217,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1155363	0.83[AMR][1000 genomes]
rs171157	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2208281	0.83[AMR][1000 genomes]
rs238641	0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs238642	0.83[AMR][1000 genomes]
rs238645	1.00[EUR][1000 genomes]
rs238646	0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238647	0.84[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238648	1.00[EUR][1000 genomes]
rs238649	1.00[EUR][1000 genomes]
rs238650	0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238651	1.00[EUR][1000 genomes]
rs238652	0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238654	1.00[EUR][1000 genomes]
rs238655	1.00[EUR][1000 genomes]
rs238656	0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238657	1.00[EUR][1000 genomes]
rs238658	0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238659	0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs238660	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238661	1.00[EUR][1000 genomes]
rs238663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238664	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238665	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238666	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238667	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238669	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs238671	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2983601	0.83[AMR][1000 genomes]
rs2983606	0.83[AMR][1000 genomes]
rs2983643	0.83[AMR][1000 genomes]
rs3004124	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs3004129	0.83[AMR][1000 genomes]
rs3004130	0.83[AMR][1000 genomes]
rs3004131	0.83[AMR][1000 genomes]
rs3004133	0.83[AMR][1000 genomes]
rs59710211	1.00[EUR][1000 genomes]
rs8113899	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1057992	chr20:23430887-23565333	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv544215	chr20:23430887-23565333	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23486200-23489600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr20:23486200-23491200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23486800-23489800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr20:23487800-23488800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr20:23488000-23489000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr20:23488000-23489400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr20:23488000-23489600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr20:23488000-23490200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:23488000-23490600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:23488000-23490800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:23488200-23488800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:23488200-23489000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr20:23488200-23489000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr20:23488200-23489000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr20:23488200-23489800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr20:23488200-23490800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:23488400-23489400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:23488600-23490400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links