Variant report

Variant	rs73399960
Chromosome Location	chr12:105278504-105278505
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	chr12:105277401..105280097-chr12:105289750..105292051,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1038969	0.81[ASN][1000 genomes]
rs10778350	0.86[EUR][1000 genomes]
rs11112189	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11834087	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12307301	0.86[EUR][1000 genomes]
rs12320887	0.86[EUR][1000 genomes]
rs12321404	0.86[EUR][1000 genomes]
rs12579202	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12579469	0.94[ASN][1000 genomes]
rs12579505	0.91[ASN][1000 genomes]
rs12579945	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12580114	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580128	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12580794	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12581352	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12582312	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1565814	0.83[AMR][1000 genomes]
rs17036358	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17036429	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17036433	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17036489	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17036545	0.94[ASN][1000 genomes]
rs4369494	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545639	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57144501	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57685442	0.95[ASN][1000 genomes]
rs59079144	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60976244	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61129422	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61262317	0.86[EUR][1000 genomes]
rs61587191	0.86[EUR][1000 genomes]
rs7302213	0.86[EUR][1000 genomes]
rs73383408	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73383420	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73383435	0.95[ASN][1000 genomes]
rs73383439	0.90[ASN][1000 genomes]
rs73383441	0.95[ASN][1000 genomes]
rs73383467	0.94[ASN][1000 genomes]
rs73383473	0.94[ASN][1000 genomes]
rs73394174	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73394185	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73394186	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73396157	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73396159	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73399912	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73399925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399927	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399929	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399931	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399934	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73399944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399947	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73399956	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971315	0.86[EUR][1000 genomes]
rs7971613	0.86[EUR][1000 genomes]
rs7976092	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:105260800-105280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:105267800-105279600	Weak transcription	A549	lung
4	chr12:105267800-105284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:105273800-105288200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:105276400-105281800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:105277000-105280400	Strong transcription	Liver	Liver
9	chr12:105277200-105279800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:105277400-105278600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr12:105278200-105279200	Weak transcription	Pancreas	Pancrea
12	chr12:105278200-105279600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:105278200-105281000	Enhancers	Fetal Lung	lung
14	chr12:105278200-105284400	Weak transcription	Aorta	Aorta
15	chr12:105278200-105284400	Weak transcription	Gastric	stomach
16	chr12:105278400-105293200	Weak transcription	Duodenum Mucosa	Duodenum

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