Variant report

Variant	rs2593184
Chromosome Location	chr15:52189201-52189202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52137753..52140319-chr15:52187826..52190548,2	MCF-7	breast:
2	chr15:52180978..52184805-chr15:52187877..52189581,3	MCF-7	breast:
3	chr15:52189166..52191186-chr15:52194492..52196039,2	K562	blood:
4	chr15:52180532..52182090-chr15:52188947..52190668,2	MCF-7	breast:
5	chr15:52184820..52187639-chr15:52189000..52191684,2	MCF-7	breast:
6	chr15:52183407..52186313-chr15:52187408..52190347,2	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs16953082	0.90[ASN][1000 genomes]
rs16964532	0.90[ASN][1000 genomes]
rs16964555	0.90[ASN][1000 genomes]
rs16964561	0.90[ASN][1000 genomes]
rs16964579	0.90[ASN][1000 genomes]
rs16964585	0.90[ASN][1000 genomes]
rs16964596	0.90[ASN][1000 genomes]
rs16964639	0.90[ASN][1000 genomes]
rs16964645	0.90[ASN][1000 genomes]
rs1863429	0.88[AMR][1000 genomes]
rs1972419	0.94[AMR][1000 genomes]
rs1991267	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016057	0.81[AMR][1000 genomes]
rs2258248	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448810	0.81[AMR][1000 genomes]
rs2448945	0.83[AMR][1000 genomes]
rs2554354	0.94[AMR][1000 genomes]
rs2554355	0.94[AMR][1000 genomes]
rs2554358	0.81[AMR][1000 genomes]
rs2570230	0.83[AMR][1000 genomes]
rs2570243	0.92[AMR][1000 genomes]
rs2570265	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	0.92[AMR][1000 genomes]
rs2593181	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.81[AMR][1000 genomes]
rs2623245	0.94[AMR][1000 genomes]
rs2623247	0.94[AMR][1000 genomes]
rs2623251	0.94[AMR][1000 genomes]
rs2623263	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2623270	0.94[AMR][1000 genomes]
rs2623280	0.92[AMR][1000 genomes]
rs2623291	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959296	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2593184	RP11-707P17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:52167600-52192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
7	chr15:52171200-52190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:52172200-52190200	Weak transcription	Fetal Heart	heart
9	chr15:52172200-52192000	Weak transcription	Fetal Brain Male	brain
10	chr15:52172800-52208200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:52177000-52189800	Weak transcription	Colonic Mucosa	Colon
12	chr15:52177000-52192400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:52177000-52192400	Weak transcription	Gastric	stomach
14	chr15:52177000-52192400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:52177200-52192400	Weak transcription	Psoas Muscle	Psoas
16	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:52177400-52190000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:52178600-52192400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:52178800-52192400	Weak transcription	Spleen	Spleen
20	chr15:52178800-52216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:52179000-52192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:52179000-52196400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52179000-52196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:52179000-52196600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:52179600-52203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:52179800-52196000	Strong transcription	HSMM	muscle
28	chr15:52179800-52197200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:52179800-52197400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:52179800-52201600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:52180000-52197400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:52180200-52199400	Strong transcription	NHEK	skin
34	chr15:52180400-52218200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:52180800-52191400	Weak transcription	Pancreas	Pancrea
36	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr15:52181400-52197000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:52181600-52190200	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:52181600-52196200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:52181600-52196200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:52181600-52197400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr15:52181600-52197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:52181600-52203400	Strong transcription	Dnd41	blood
44	chr15:52181800-52195600	Strong transcription	A549	lung
45	chr15:52181800-52203400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:52182600-52192400	Weak transcription	Esophagus	oesophagus
47	chr15:52182800-52198600	Strong transcription	HMEC	breast
48	chr15:52183000-52203400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:52183400-52203200	Strong transcription	Primary T cells from cord blood	blood

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