Variant report

Variant	rs2497727
Chromosome Location	chr10:116314035-116314036
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116229710..116232429-chr10:116312044..116314451,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10787538	0.84[AFR][1000 genomes]
rs10885581	0.84[AFR][1000 genomes]
rs1333688	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483534	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483537	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483538	0.87[AMR][1000 genomes]
rs2483539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483543	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2483546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483549	0.87[AMR][1000 genomes]
rs2483550	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483557	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483558	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483560	0.86[AMR][1000 genomes]
rs2483573	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2483590	0.82[AMR][1000 genomes]
rs2497724	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2497725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497726	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497729	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497732	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2497733	0.87[AMR][1000 genomes]
rs2497735	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2497737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497739	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497740	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2497741	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497742	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497743	0.85[AMR][1000 genomes]
rs2497744	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128920	0.83[AMR][1000 genomes]
rs7085345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7091986	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7913199	0.83[AMR][1000 genomes]
rs7915116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7915301	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7915452	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9325544	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9421186	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116305000-116317600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:116305200-116316000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:116305200-116318200	Weak transcription	Fetal Intestine Large	intestine
4	chr10:116307600-116316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:116307800-116317600	Weak transcription	Fetal Intestine Small	intestine
6	chr10:116308600-116315800	Weak transcription	HepG2	liver
7	chr10:116309000-116316400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:116310800-116317400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:116311000-116317400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:116311000-116331400	Weak transcription	Fetal Brain Male	brain
11	chr10:116311600-116336600	Weak transcription	Colonic Mucosa	Colon
12	chr10:116311800-116317800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:116312000-116316800	Weak transcription	Lung	lung
14	chr10:116312000-116317200	Enhancers	Fetal Heart	heart
15	chr10:116312000-116324800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:116312000-116331000	Weak transcription	Ovary	ovary
17	chr10:116312000-116334600	Weak transcription	Esophagus	oesophagus
18	chr10:116312000-116335000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr10:116312000-116335200	Weak transcription	Pancreas	Pancrea
20	chr10:116312200-116315800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:116312200-116317600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:116312200-116330800	Weak transcription	Adipose Nuclei	Adipose
23	chr10:116312400-116314600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:116312400-116315400	Weak transcription	Stomach Mucosa	stomach
25	chr10:116312400-116316000	Weak transcription	Psoas Muscle	Psoas
26	chr10:116312400-116316800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:116312400-116316800	Weak transcription	HSMM	muscle
28	chr10:116312400-116331200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:116312600-116316000	Weak transcription	Liver	Liver
30	chr10:116312800-116315200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:116312800-116317400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:116313000-116317600	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:116313000-116319200	Genic enhancers	Left Ventricle	heart
34	chr10:116313200-116314200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:116313400-116314400	Enhancers	Right Atrium	heart
36	chr10:116313400-116316000	Weak transcription	HSMMtube	muscle
37	chr10:116313600-116314200	Weak transcription	Brain Substantia Nigra	brain
38	chr10:116313600-116314800	Enhancers	Right Ventricle	heart
39	chr10:116314000-116316000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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