Variant report

Variant	rs12471646
Chromosome Location	chr2:152775308-152775309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152774772..152776597-chr2:152777581..152779285,2	MCF-7	breast:
2	chr2:152774858..152777174-chr2:152778629..152781508,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11695363	1.00[YRI][hapmap]
rs12472173	0.86[ASW][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs12992504	0.86[ASW][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs13394161	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1401780	0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1519713	0.82[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs17270332	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2461835	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2680976	0.80[AMR][1000 genomes]
rs35343813	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36052741	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4524119	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664067	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4664508	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664514	0.90[JPT][hapmap]
rs6433733	0.82[JPT][hapmap]
rs6727592	0.82[JPT][hapmap]
rs6729612	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729655	0.80[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6734642	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6748807	0.80[AMR][1000 genomes]
rs6751763	0.82[JPT][hapmap]
rs7349251	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7558481	0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs7564060	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7565405	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7571637	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7584868	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7598593	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7602165	0.86[ASW][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs952340	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs956745	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152765200-152778800	Weak transcription	Brain Anterior Caudate	brain
2	chr2:152765400-152777600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:152767800-152780400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:152771800-152778800	Weak transcription	Psoas Muscle	Psoas
5	chr2:152771800-152779400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:152772600-152775800	Weak transcription	Lung	lung
7	chr2:152773200-152776000	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:152773400-152775800	Weak transcription	Placenta	Placenta
9	chr2:152773400-152776400	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:152773400-152779000	Weak transcription	Right Atrium	heart
11	chr2:152773600-152779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:152774200-152775600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr2:152774400-152775600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:152774400-152776400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:152774400-152776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:152774600-152776600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:152774800-152775400	Enhancers	Primary T cells from cord blood	blood
18	chr2:152774800-152775400	Enhancers	Fetal Heart	heart
19	chr2:152774800-152776600	Enhancers	Primary B cells from cord blood	blood
20	chr2:152775000-152775400	Enhancers	Left Ventricle	heart
21	chr2:152775000-152775800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:152775000-152776200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:152775200-152775600	Weak transcription	Spleen	Spleen
24	chr2:152775200-152775800	Enhancers	Adipose Nuclei	Adipose
25	chr2:152775200-152776000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:152775200-152776200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:152775200-152776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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