Variant report

Variant	rs2966901
Chromosome Location	chr5:12238948-12238949
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	chr5:12237914..12240147-chr5:12240749..12242616,3	MCF-7	breast:
2	chr5:12232884..12235598-chr5:12236821..12239315,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12657630	0.84[AMR][1000 genomes]
rs12658793	0.84[AMR][1000 genomes]
rs1468537	0.82[AMR][1000 genomes]
rs17210105	0.84[AMR][1000 genomes]
rs17210112	0.83[AMR][1000 genomes]
rs17823762	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808270	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024139	0.84[AMR][1000 genomes]
rs2079689	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2191014	0.87[AMR][1000 genomes]
rs2215253	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2400148	0.84[AMR][1000 genomes]
rs2907084	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2907273	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2907278	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2907280	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2966902	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968089	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968091	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968102	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968103	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2968121	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968122	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32285	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4260673	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4702855	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4702867	0.88[AMR][1000 genomes]
rs4702869	0.84[AMR][1000 genomes]
rs56104855	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56236505	0.88[AMR][1000 genomes]
rs59391977	0.88[AMR][1000 genomes]
rs60419314	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62338055	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62349366	0.88[AMR][1000 genomes]
rs62349369	0.83[AMR][1000 genomes]
rs62349370	0.90[AMR][1000 genomes]
rs62349371	0.88[AMR][1000 genomes]
rs62349372	0.90[AMR][1000 genomes]
rs6420013	0.83[AMR][1000 genomes]
rs6870511	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6871226	0.83[AMR][1000 genomes]
rs6874191	0.81[EUR][1000 genomes]
rs6875403	0.81[EUR][1000 genomes]
rs6890244	0.84[AMR][1000 genomes]
rs7735051	0.81[AMR][1000 genomes]
rs969805	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][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	nsv597155	chr5:12022698-12251916	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1016098	chr5:12042741-12310988	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470989	chr5:12110214-12288541	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv880440	chr5:12128980-12288541	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv880704	chr5:12132401-12338203	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv881603	chr5:12153033-12288541	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv880364	chr5:12153033-12330841	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1024189	chr5:12162849-12258950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv537663	chr5:12162849-12258950	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1030593	chr5:12183469-12250607	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1023330	chr5:12217960-12285735	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1031406	chr5:12231297-12305842	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12236600-12239400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:12237200-12239000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr5:12237600-12239000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr5:12237600-12239200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:12237600-12239200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr5:12238000-12239200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr5:12238000-12239200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr5:12238000-12239200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr5:12238000-12239200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr5:12238600-12239200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:12238600-12239200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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