Variant report

Variant	rs11054616
Chromosome Location	chr12:12173973-12173974
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	chr12:12161417..12164004-chr12:12173904..12175896,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10845451	0.96[ASN][1000 genomes]
rs10845452	0.96[ASN][1000 genomes]
rs10845453	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054619	0.96[ASN][1000 genomes]
rs12146841	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12424479	0.84[AMR][1000 genomes]
rs12425503	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12426754	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28720964	1.00[ASN][1000 genomes]
rs59213608	0.96[ASN][1000 genomes]
rs60058224	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73285722	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73285733	0.84[AMR][1000 genomes];0.82[EUR][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898804	chr12:12058411-12202173	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12164800-12179800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:12170000-12176800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:12170400-12175600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:12170600-12176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:12170600-12177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:12170600-12177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:12170800-12176400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:12170800-12179200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:12171200-12176400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:12171200-12185400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:12171400-12174600	Weak transcription	GM12878-XiMat	blood
12	chr12:12171400-12175400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:12171400-12175400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:12171400-12185200	Weak transcription	Spleen	Spleen
15	chr12:12171600-12175400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:12171600-12175400	Weak transcription	Fetal Thymus	thymus
17	chr12:12171800-12175800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:12171800-12185000	Weak transcription	Esophagus	oesophagus
19	chr12:12172200-12175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:12172200-12175600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:12172200-12184600	Weak transcription	Thymus	Thymus
22	chr12:12173200-12178200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:12173400-12174200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:12173600-12174000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr12:12173600-12174000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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