Variant report

Variant	rs12999865
Chromosome Location	chr2:233627250-233627251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233625989..233627596-chr2:233662051..233663810,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10210953	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1022329	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10427328	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1078323	0.80[EUR][1000 genomes]
rs10933406	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1104764	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11688166	0.82[EUR][1000 genomes]
rs11689851	0.82[EUR][1000 genomes]
rs11893358	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12105766	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619195	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12993791	0.81[EUR][1000 genomes]
rs13001052	0.80[EUR][1000 genomes]
rs17164	0.84[EUR][1000 genomes]
rs1973675	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293780	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2344611	0.83[EUR][1000 genomes]
rs2344613	0.84[EUR][1000 genomes]
rs2592104	0.85[EUR][1000 genomes]
rs2675972	0.80[EUR][1000 genomes]
rs283470	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs283487	0.87[EUR][1000 genomes]
rs35491427	0.81[EUR][1000 genomes]
rs62193269	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62193271	0.82[EUR][1000 genomes]
rs6704763	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710294	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6716488	0.84[EUR][1000 genomes]
rs6717048	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733495	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6739794	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737027	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs974321	0.87[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:233571200-233627400	Weak transcription	Gastric	stomach
3	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
5	chr2:233602400-233633200	Weak transcription	Aorta	Aorta
6	chr2:233606200-233638400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:233606800-233633200	Weak transcription	Stomach Mucosa	stomach
8	chr2:233606800-233636800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:233609200-233630800	Strong transcription	HepG2	liver
10	chr2:233611000-233628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:233611600-233645600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:233612000-233631000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:233612000-233634000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:233612000-233634000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:233612000-233640000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:233612000-233644600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:233612200-233633800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:233612200-233634000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:233612200-233634400	Strong transcription	Fetal Thymus	thymus
20	chr2:233612200-233638400	Strong transcription	Placenta	Placenta
21	chr2:233612600-233637200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:233613600-233627400	Weak transcription	Ovary	ovary
23	chr2:233613800-233635600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:233614000-233628800	Weak transcription	Fetal Brain Male	brain
25	chr2:233614000-233636800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:233614400-233632800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:233614600-233643600	Weak transcription	Small Intestine	intestine
28	chr2:233615800-233627600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:233616200-233627400	Weak transcription	Spleen	Spleen
30	chr2:233616800-233628400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:233617000-233627600	Weak transcription	NHLF	lung
32	chr2:233617000-233636600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:233617200-233627400	Weak transcription	Fetal Kidney	kidney
34	chr2:233617200-233628800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:233617400-233627400	Weak transcription	Brain Anterior Caudate	brain
36	chr2:233618400-233629000	Weak transcription	Right Ventricle	heart
37	chr2:233618600-233627400	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:233618600-233635600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:233620000-233627400	Weak transcription	Hela-S3	cervix
40	chr2:233620200-233640000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:233620600-233627400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:233621400-233627400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:233621400-233632400	Weak transcription	K562	blood
44	chr2:233621400-233644400	Strong transcription	Liver	Liver
45	chr2:233621600-233627400	Weak transcription	Fetal Brain Female	brain
46	chr2:233621600-233627400	Weak transcription	Lung	lung
47	chr2:233621800-233627400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:233622000-233627600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:233622400-233635600	Weak transcription	Esophagus	oesophagus
50	chr2:233622600-233627400	Weak transcription	Brain Substantia Nigra	brain

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