Variant report

Variant	rs73407817
Chromosome Location	chr15:55466424-55466425
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	chr10:13366886..13368696-chr15:55465125..55467342,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSL24D1-1	chr15:55464171-55468937	ENSG00000248800

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

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047995	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10152400	0.97[EUR][1000 genomes]
rs10518800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11852793	0.94[EUR][1000 genomes]
rs11853315	0.81[EUR][1000 genomes]
rs11855490	0.86[EUR][1000 genomes]
rs11858001	0.97[EUR][1000 genomes]
rs16976069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16976076	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414403	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28565375	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524935	0.94[EUR][1000 genomes]
rs58922764	0.97[EUR][1000 genomes]
rs59357544	0.94[EUR][1000 genomes]
rs59683414	0.86[EUR][1000 genomes]
rs60802234	0.97[EUR][1000 genomes]
rs6493764	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493765	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7163677	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7168226	0.86[EUR][1000 genomes]
rs7169357	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73404044	0.86[EUR][1000 genomes]
rs73404055	0.86[EUR][1000 genomes]
rs73404072	0.94[EUR][1000 genomes]
rs73404076	0.94[EUR][1000 genomes]
rs73404078	0.94[EUR][1000 genomes]
rs73404093	0.94[EUR][1000 genomes]
rs73405810	0.97[EUR][1000 genomes]
rs73405811	0.97[EUR][1000 genomes]
rs73405825	0.97[EUR][1000 genomes]
rs73405883	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73405887	0.97[EUR][1000 genomes]
rs73405889	0.97[EUR][1000 genomes]
rs73405890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73405894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405898	0.97[EUR][1000 genomes]
rs73407805	0.98[AFR][1000 genomes]
rs73407806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407816	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407821	0.97[EUR][1000 genomes]
rs73407823	0.97[EUR][1000 genomes]
rs73407850	0.89[EUR][1000 genomes]
rs73409840	0.89[EUR][1000 genomes]
rs74015506	0.89[EUR][1000 genomes]
rs74018312	0.86[EUR][1000 genomes]
rs8026190	0.81[EUR][1000 genomes]
rs8038091	0.94[EUR][1000 genomes]
rs8042411	0.94[EUR][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	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455600-55469600	Weak transcription	Aorta	Aorta
2	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:55459000-55469800	Weak transcription	HSMM	muscle
4	chr15:55461000-55469200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:55462600-55470200	Weak transcription	Fetal Lung	lung
6	chr15:55462600-55471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:55463200-55470400	Weak transcription	A549	lung
9	chr15:55463200-55472400	Weak transcription	Ovary	ovary
10	chr15:55463200-55474600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:55463400-55472200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:55463800-55472600	Weak transcription	Fetal Kidney	kidney
13	chr15:55464000-55470800	Weak transcription	Brain Germinal Matrix	brain
14	chr15:55464400-55469000	Weak transcription	Primary T cells from cord blood	blood
15	chr15:55464400-55470600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:55464600-55472400	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:55464800-55488200	Weak transcription	Lung	lung
18	chr15:55465000-55469600	Weak transcription	Primary B cells from cord blood	blood
19	chr15:55465200-55470400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:55465200-55470800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:55465400-55469800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:55465400-55469800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:55465400-55470400	Weak transcription	Dnd41	blood
24	chr15:55465400-55470800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:55465400-55471000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:55465400-55471200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:55465400-55471400	Weak transcription	Brain Angular Gyrus	brain
28	chr15:55465400-55472600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:55465400-55476600	Weak transcription	Brain Anterior Caudate	brain
30	chr15:55465600-55470000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:55465600-55470000	Weak transcription	Adipose Nuclei	Adipose
32	chr15:55465600-55470200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:55465600-55470400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:55465600-55470400	Weak transcription	Left Ventricle	heart
35	chr15:55465800-55467400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:55465800-55469400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:55465800-55470200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:55465800-55471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:55466000-55469200	Weak transcription	Liver	Liver
40	chr15:55466200-55466800	Strong transcription	Psoas Muscle	Psoas
41	chr15:55466200-55470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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