Variant report

Variant	rs2554329
Chromosome Location	chr15:52154732-52154733
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52120607..52125174-chr15:52151783..52155506,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11446467	0.83[AFR][1000 genomes]
rs1426085	0.81[AFR][1000 genomes]
rs1824083	0.82[YRI][hapmap]
rs1867985	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2162224	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2263946	0.81[AFR][1000 genomes]
rs2436663	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2436664	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2470592	0.91[YRI][hapmap]
rs2470606	0.84[AFR][1000 genomes]
rs2554310	0.84[YRI][hapmap]
rs2554311	0.81[AFR][1000 genomes]
rs2554312	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554319	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2554320	0.93[AFR][1000 genomes]
rs2554321	0.91[YRI][hapmap]
rs2554323	0.81[AFR][1000 genomes]
rs2554324	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554325	0.84[AFR][1000 genomes]
rs2554330	0.85[AFR][1000 genomes]
rs2554331	0.91[YRI][hapmap]
rs2554333	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2554341	0.91[YRI][hapmap]
rs2554344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554346	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554351	0.87[AFR][1000 genomes]
rs2554352	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2554356	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554357	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs2570218	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2570220	0.81[AFR][1000 genomes]
rs2570221	0.81[AFR][1000 genomes]
rs2570222	0.93[AFR][1000 genomes]
rs2570223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570227	0.84[AFR][1000 genomes]
rs2570232	1.00[YRI][hapmap]
rs2570242	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570244	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2570245	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570246	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570247	0.87[AFR][1000 genomes]
rs2570249	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570250	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570256	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570257	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570259	0.83[AFR][1000 genomes]
rs2570261	0.87[AFR][1000 genomes]
rs2570266	0.93[AFR][1000 genomes]
rs2570267	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570270	0.91[YRI][hapmap]
rs2570272	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570273	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593165	0.81[AFR][1000 genomes]
rs2593171	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2593172	0.93[AFR][1000 genomes]
rs2593175	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593176	0.81[AFR][1000 genomes]
rs2593178	0.90[AFR][1000 genomes]
rs2593180	0.81[AFR][1000 genomes]
rs2593186	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2593203	0.84[AFR][1000 genomes]
rs2623246	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623248	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623250	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623252	0.87[AFR][1000 genomes]
rs2623264	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623267	0.84[AFR][1000 genomes]
rs2623269	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623274	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623277	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623278	0.81[AFR][1000 genomes]
rs2623287	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623290	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2623293	0.92[YRI][hapmap]
rs2652596	0.81[YRI][hapmap]
rs2916174	0.81[AFR][1000 genomes]
rs543024	0.81[YRI][hapmap]
rs562858	0.82[YRI][hapmap]
rs689842	0.83[YRI][hapmap]
rs690433	0.83[YRI][hapmap]
rs73396698	0.81[AFR][1000 genomes]
rs73411105	0.87[AFR][1000 genomes]
rs919056	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs919057	0.91[YRI][hapmap]
rs919058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs990666	0.91[YRI][hapmap]

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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:52135800-52155000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:52136000-52155200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:52136200-52155000	Weak transcription	Aorta	Aorta
6	chr15:52137800-52155000	Weak transcription	Fetal Intestine Large	intestine
7	chr15:52138000-52155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:52138600-52155000	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
10	chr15:52139400-52156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:52139600-52154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:52140000-52155000	Weak transcription	NH-A	brain
13	chr15:52140200-52155400	Weak transcription	HSMMtube	muscle
14	chr15:52140400-52155000	Weak transcription	HSMM	muscle
15	chr15:52140600-52155400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52141400-52155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:52141600-52155000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
19	chr15:52141800-52155000	Weak transcription	Fetal Stomach	stomach
20	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:52142200-52155400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:52144200-52155000	Weak transcription	K562	blood
23	chr15:52145000-52156600	Weak transcription	Fetal Brain Female	brain
24	chr15:52145600-52155000	Weak transcription	Placenta	Placenta
25	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
26	chr15:52146600-52155200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:52147400-52155000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:52148000-52155000	Weak transcription	Osteobl	bone
29	chr15:52148200-52155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:52148200-52157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:52148400-52155200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:52148600-52155000	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:52148600-52155000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:52149000-52161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:52149200-52155400	Weak transcription	Ovary	ovary
37	chr15:52149200-52156200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:52149400-52154800	Weak transcription	NHLF	lung
39	chr15:52149400-52155000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:52149400-52156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
42	chr15:52149600-52155000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:52149600-52155000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:52149600-52155000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:52149600-52155200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:52149600-52155200	Weak transcription	Liver	Liver
47	chr15:52149600-52155200	Weak transcription	Brain Anterior Caudate	brain
48	chr15:52149600-52155600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:52149600-52156800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr15:52149800-52154800	Weak transcription	NHDF-Ad	bronchial

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