Variant report

Variant	rs1972419
Chromosome Location	chr15:52152859-52152860
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	chr15:52120607..52125174-chr15:52151783..52155506,6	MCF-7	breast:
2	chr15:52120409..52123453-chr15:52147332..52153488,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1133878	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[ASN][1000 genomes]
rs16964483	1.00[ASN][1000 genomes]
rs17611465	1.00[ASN][1000 genomes]
rs1863429	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991267	0.92[AMR][1000 genomes]
rs2016057	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	0.82[AMR][1000 genomes]
rs2448810	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2554354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570230	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570265	0.87[AMR][1000 genomes]
rs2593169	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593181	0.89[AMR][1000 genomes]
rs2593184	0.94[AMR][1000 genomes]
rs2606128	0.81[AMR][1000 genomes]
rs2606130	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[ASN][1000 genomes]
rs2623245	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623258	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623291	0.87[AMR][1000 genomes]
rs2652595	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.84[AMR][1000 genomes]
rs28501427	1.00[ASN][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28718531	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	0.83[AMR][1000 genomes]
rs55922236	1.00[ASN][1000 genomes]
rs691738	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]
rs8024265	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

No data

Chromatin state (count:107 , 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	chr15:52136600-52153400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:52137800-52155000	Weak transcription	Fetal Intestine Large	intestine
8	chr15:52138000-52153400	Weak transcription	Esophagus	oesophagus
9	chr15:52138000-52155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:52138600-52155000	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:52139000-52153400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:52139400-52156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:52139600-52154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:52139800-52153400	Weak transcription	Fetal Thymus	thymus
16	chr15:52139800-52153600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:52140000-52155000	Weak transcription	NH-A	brain
18	chr15:52140200-52155400	Weak transcription	HSMMtube	muscle
19	chr15:52140400-52155000	Weak transcription	HSMM	muscle
20	chr15:52140600-52155400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:52141400-52155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:52141600-52155000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
24	chr15:52141800-52154000	Weak transcription	Adipose Nuclei	Adipose
25	chr15:52141800-52155000	Weak transcription	Fetal Stomach	stomach
26	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:52142200-52155400	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:52143200-52153400	Weak transcription	Spleen	Spleen
29	chr15:52143400-52153400	Weak transcription	Right Atrium	heart
30	chr15:52144200-52153400	Weak transcription	Lung	lung
31	chr15:52144200-52155000	Weak transcription	K562	blood
32	chr15:52145000-52153200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:52145000-52156600	Weak transcription	Fetal Brain Female	brain
34	chr15:52145400-52153800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:52145600-52153400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:52145600-52155000	Weak transcription	Placenta	Placenta
37	chr15:52145800-52154000	Weak transcription	Left Ventricle	heart
38	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
39	chr15:52146400-52153600	Weak transcription	Small Intestine	intestine
40	chr15:52146600-52153200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52146600-52155200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:52147400-52155000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:52147600-52153800	Weak transcription	Gastric	stomach
44	chr15:52148000-52155000	Weak transcription	Osteobl	bone
45	chr15:52148200-52153400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:52148200-52153400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:52148200-52155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52148200-52157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:52148400-52155200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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