Variant report

Variant	rs2554357
Chromosome Location	chr15:52108737-52108738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52107930..52111784-chr15:52120975..52124662,5	MCF-7	breast:
2	chr15:52106284..52108941-chr15:52129387..52131261,2	MCF-7	breast:
3	chr15:52089329..52092071-chr15:52108088..52110534,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10519324	1.00[EUR][1000 genomes]
rs16953079	1.00[EUR][1000 genomes]
rs16964509	1.00[EUR][1000 genomes]
rs16964513	1.00[EUR][1000 genomes]
rs16964517	1.00[EUR][1000 genomes]
rs16964530	1.00[EUR][1000 genomes]
rs17649601	1.00[EUR][1000 genomes]
rs1824083	0.86[YRI][hapmap]
rs1867985	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2162224	0.92[YRI][hapmap]
rs2436663	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2436664	0.94[YRI][hapmap]
rs2470592	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2470606	0.88[AFR][1000 genomes]
rs2470614	0.83[AFR][1000 genomes]
rs2554310	0.82[YRI][hapmap]
rs2554312	0.85[AFR][1000 genomes]
rs2554319	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2554320	0.85[AFR][1000 genomes]
rs2554321	0.87[YRI][hapmap]
rs2554324	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2554329	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs2554331	0.80[YRI][hapmap]
rs2554333	0.94[YRI][hapmap]
rs2554341	0.87[YRI][hapmap]
rs2554344	0.85[AFR][1000 genomes]
rs2554346	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2554352	0.94[YRI][hapmap]
rs2554356	0.94[YRI][hapmap]
rs2570218	0.93[YRI][hapmap]
rs2570222	0.85[AFR][1000 genomes]
rs2570223	0.85[AFR][1000 genomes]
rs2570232	0.93[YRI][hapmap]
rs2570242	0.93[YRI][hapmap]
rs2570244	0.94[YRI][hapmap]
rs2570245	0.94[YRI][hapmap]
rs2570246	0.94[YRI][hapmap]
rs2570249	0.93[YRI][hapmap]
rs2570250	0.93[YRI][hapmap]
rs2570256	0.94[YRI][hapmap]
rs2570257	0.94[YRI][hapmap]
rs2570266	0.85[AFR][1000 genomes]
rs2570267	0.94[YRI][hapmap]
rs2570270	1.00[YRI][hapmap]
rs2570272	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2570273	0.93[YRI][hapmap]
rs2593171	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2593172	0.85[AFR][1000 genomes]
rs2593175	0.94[YRI][hapmap]
rs2593178	0.82[AFR][1000 genomes]
rs2593186	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2593203	0.88[AFR][1000 genomes]
rs2623246	0.94[YRI][hapmap]
rs2623248	0.94[YRI][hapmap]
rs2623250	0.93[YRI][hapmap]
rs2623264	0.93[YRI][hapmap]
rs2623269	0.94[YRI][hapmap]
rs2623273	0.85[AFR][1000 genomes]
rs2623274	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2623275	0.85[AFR][1000 genomes]
rs2623277	0.94[YRI][hapmap]
rs2623287	0.93[YRI][hapmap]
rs2623290	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2623293	0.88[YRI][hapmap]
rs2652596	0.86[YRI][hapmap]
rs543024	0.86[YRI][hapmap]
rs562858	0.86[YRI][hapmap]
rs58356723	1.00[EUR][1000 genomes]
rs58958163	1.00[EUR][1000 genomes]
rs59522140	1.00[EUR][1000 genomes]
rs689842	0.87[YRI][hapmap]
rs690433	0.87[YRI][hapmap]
rs73396698	0.85[AFR][1000 genomes]
rs73405368	1.00[EUR][1000 genomes]
rs73405370	1.00[EUR][1000 genomes]
rs73405377	1.00[EUR][1000 genomes]
rs73405389	1.00[EUR][1000 genomes]
rs73405400	1.00[EUR][1000 genomes]
rs73407328	1.00[EUR][1000 genomes]
rs73407332	1.00[EUR][1000 genomes]
rs73407339	1.00[EUR][1000 genomes]
rs73407384	1.00[EUR][1000 genomes]
rs73407392	1.00[EUR][1000 genomes]
rs73407393	1.00[EUR][1000 genomes]
rs73409029	1.00[EUR][1000 genomes]
rs73409034	1.00[EUR][1000 genomes]
rs919056	0.81[YRI][hapmap]
rs919057	0.87[YRI][hapmap]
rs919058	0.85[AFR][1000 genomes]
rs990666	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52061600-52112000	Weak transcription	NHLF	lung
2	chr15:52085800-52108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:52091200-52109400	Weak transcription	Gastric	stomach
4	chr15:52098800-52108800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:52099200-52108800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:52099600-52108800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:52099800-52109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:52099800-52109400	Weak transcription	Spleen	Spleen
9	chr15:52099800-52110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:52099800-52110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:52099800-52110400	Weak transcription	Left Ventricle	heart
12	chr15:52099800-52113800	Weak transcription	Aorta	Aorta
13	chr15:52100000-52109400	Weak transcription	Esophagus	oesophagus
14	chr15:52100000-52109400	Weak transcription	Fetal Stomach	stomach
15	chr15:52100000-52109400	Weak transcription	Lung	lung
16	chr15:52100000-52110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:52100000-52113200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:52100200-52109400	Weak transcription	Fetal Brain Female	brain
19	chr15:52100600-52109800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:52101200-52108800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:52101200-52110200	Weak transcription	NHDF-Ad	bronchial
22	chr15:52101600-52113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:52101800-52110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:52102000-52113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:52102400-52109000	Weak transcription	Adipose Nuclei	Adipose
26	chr15:52103000-52109000	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:52103000-52111600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr15:52104400-52113400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:52104400-52113600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:52105600-52113200	Weak transcription	Primary B cells from cord blood	blood
31	chr15:52105800-52111600	Weak transcription	Thymus	Thymus
32	chr15:52106600-52111800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:52106800-52108800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:52106800-52110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52106800-52113400	Weak transcription	Brain Germinal Matrix	brain
36	chr15:52107000-52110600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:52107000-52113200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:52107000-52113600	Weak transcription	Primary T cells from cord blood	blood
39	chr15:52107000-52113800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:52107200-52112800	Weak transcription	Brain Angular Gyrus	brain
41	chr15:52107200-52113000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:52107200-52121400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:52107400-52108800	Enhancers	K562	blood
44	chr15:52107600-52109600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:52107600-52109800	Enhancers	Liver	Liver
46	chr15:52108000-52110000	Enhancers	Fetal Intestine Small	intestine
47	chr15:52108200-52110000	Enhancers	Fetal Intestine Large	intestine
48	chr15:52108600-52109200	Enhancers	HepG2	liver
49	chr15:52108600-52109400	Enhancers	Fetal Lung	lung
50	chr15:52108600-52109400	Enhancers	HUVEC	blood vessel

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