Variant report

Variant	rs12659887
Chromosome Location	chr5:5442342-5442343
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	chr5:5423692..5425545-chr5:5442007..5444418,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10036927	1.00[MEX][hapmap]
rs10064182	1.00[TSI][hapmap]
rs13179772	1.00[MEX][hapmap]
rs16875123	1.00[TSI][hapmap]
rs41407144	1.00[MEX][hapmap]
rs41524744	1.00[MEX][hapmap]
rs41528844	1.00[MEX][hapmap]
rs4398607	1.00[MEX][hapmap]
rs60016681	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60221804	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000446	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643751	0.93[EUR][1000 genomes]
rs72643752	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643753	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72643754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs747515	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[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	nsv1021802	chr5:5415877-5452886	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv528309	chr5:5434937-5452839	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5425000-5443600	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:5425200-5443200	Weak transcription	Fetal Brain Male	brain
3	chr5:5425200-5443600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:5425200-5443600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:5425200-5443600	Weak transcription	Pancreas	Pancrea
6	chr5:5425200-5443800	Weak transcription	Esophagus	oesophagus
7	chr5:5425400-5443600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:5425400-5443800	Weak transcription	Colonic Mucosa	Colon
9	chr5:5425600-5443400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:5425600-5443400	Weak transcription	Brain Germinal Matrix	brain
11	chr5:5425600-5443600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:5425600-5443600	Weak transcription	Thymus	Thymus
13	chr5:5425800-5443200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:5426000-5443200	Weak transcription	Brain Anterior Caudate	brain
15	chr5:5428000-5444800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:5428400-5443600	Weak transcription	Right Ventricle	heart
17	chr5:5429600-5443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:5430200-5478800	Weak transcription	Stomach Mucosa	stomach
19	chr5:5430400-5443600	Weak transcription	Gastric	stomach
20	chr5:5430400-5443600	Weak transcription	Lung	lung
21	chr5:5430800-5460800	Weak transcription	Fetal Heart	heart
22	chr5:5432600-5443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:5432800-5443400	Weak transcription	HMEC	breast
24	chr5:5432800-5443600	Weak transcription	NHEK	skin
25	chr5:5433200-5443200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:5433200-5456800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:5433400-5443600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:5433400-5443600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:5433400-5443600	Weak transcription	Spleen	Spleen
30	chr5:5433400-5444400	Weak transcription	HUVEC	blood vessel
31	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:5433600-5443600	Weak transcription	Aorta	Aorta
33	chr5:5433600-5443600	Weak transcription	Brain Substantia Nigra	brain
34	chr5:5433600-5443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:5433600-5447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:5433600-5455400	Weak transcription	Small Intestine	intestine
37	chr5:5433800-5443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:5433800-5443400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:5433800-5443600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:5433800-5443600	Weak transcription	Brain Angular Gyrus	brain
41	chr5:5433800-5444800	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:5434000-5443600	Weak transcription	Ovary	ovary
43	chr5:5434000-5443600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr5:5434000-5443600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:5434000-5460000	Weak transcription	Psoas Muscle	Psoas
46	chr5:5434600-5443400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:5434600-5446000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:5435000-5454200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr5:5435400-5443400	Weak transcription	Fetal Brain Female	brain
50	chr5:5436600-5468400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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