Variant report

Variant	rs12868469
Chromosome Location	chr13:30374060-30374061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30373480..30375303-chr13:30379875..30382396,3	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12859613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12861019	0.85[EUR][1000 genomes]
rs12864739	0.85[EUR][1000 genomes]
rs12865525	0.85[EUR][1000 genomes]
rs12867537	0.85[EUR][1000 genomes]
rs12868298	0.85[EUR][1000 genomes]
rs12869325	1.00[AMR][1000 genomes]
rs12869833	0.85[EUR][1000 genomes]
rs12872768	0.81[EUR][1000 genomes]
rs12874615	0.85[EUR][1000 genomes]
rs12875231	0.81[EUR][1000 genomes]
rs12877107	0.85[EUR][1000 genomes]
rs1631987	0.85[EUR][1000 genomes]
rs166760	0.85[EUR][1000 genomes]
rs17073897	0.82[EUR][1000 genomes]
rs17073905	0.85[EUR][1000 genomes]
rs17073919	0.85[EUR][1000 genomes]
rs1747057	0.85[EUR][1000 genomes]
rs1747060	0.85[EUR][1000 genomes]
rs1747061	0.85[EUR][1000 genomes]
rs1747062	0.85[EUR][1000 genomes]
rs1747063	0.85[EUR][1000 genomes]
rs17502757	0.85[EUR][1000 genomes]
rs1772726	0.85[EUR][1000 genomes]
rs2256122	0.84[EUR][1000 genomes]
rs2476650	0.84[EUR][1000 genomes]
rs2476651	0.88[EUR][1000 genomes]
rs2761929	0.85[EUR][1000 genomes]
rs2761930	0.85[EUR][1000 genomes]
rs2761931	0.88[EUR][1000 genomes]
rs2761932	0.85[EUR][1000 genomes]
rs2761934	0.88[EUR][1000 genomes]
rs2761936	0.85[EUR][1000 genomes]
rs278031	0.85[EUR][1000 genomes]
rs278032	0.85[EUR][1000 genomes]
rs278033	0.85[EUR][1000 genomes]
rs278035	0.85[EUR][1000 genomes]
rs278036	0.85[EUR][1000 genomes]
rs278039	0.85[EUR][1000 genomes]
rs2794295	0.85[EUR][1000 genomes]
rs2794297	0.82[EUR][1000 genomes]
rs2794300	0.85[EUR][1000 genomes]
rs3118079	0.85[EUR][1000 genomes]
rs3118080	0.85[EUR][1000 genomes]
rs34114731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34129219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34232669	0.85[EUR][1000 genomes]
rs34317115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34333613	0.84[EUR][1000 genomes]
rs34726132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34837672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34943308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35042630	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35158864	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35177317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35452290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35520191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35693706	0.85[EUR][1000 genomes]
rs35727212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35735441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35828457	0.85[EUR][1000 genomes]
rs35849390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35889915	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35933528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36082926	0.85[EUR][1000 genomes]
rs57634252	0.85[EUR][1000 genomes]
rs71427282	0.85[EUR][1000 genomes]
rs71434756	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71434758	0.85[EUR][1000 genomes]
rs71434759	1.00[EUR][1000 genomes]
rs71434760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71434762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71434763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71434764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71434765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71434766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs719199	0.85[EUR][1000 genomes]
rs7985986	0.85[EUR][1000 genomes]
rs7992684	0.85[EUR][1000 genomes]
rs818763	0.85[EUR][1000 genomes]
rs818764	0.85[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	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:30362400-30375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:30363400-30375400	Weak transcription	Lung	lung
5	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
6	chr13:30365800-30383200	Weak transcription	Ovary	ovary
7	chr13:30366000-30375200	Weak transcription	Gastric	stomach
8	chr13:30366000-30375600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
10	chr13:30368000-30375200	Weak transcription	Brain Substantia Nigra	brain
11	chr13:30368200-30375400	Weak transcription	Brain Anterior Caudate	brain
12	chr13:30368200-30375400	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:30369000-30375800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:30371000-30376000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:30371200-30375800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr13:30371800-30374200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:30371800-30375800	Weak transcription	Osteobl	bone
18	chr13:30372000-30374200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr13:30372400-30374200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr13:30372400-30374200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr13:30372400-30375000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:30372400-30375000	Weak transcription	Psoas Muscle	Psoas
23	chr13:30372800-30378000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr13:30372800-30378000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:30373000-30374200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr13:30373000-30374400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:30373000-30377800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr13:30373200-30374600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr13:30373200-30376600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr13:30373200-30377600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr13:30373400-30375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:30373400-30383200	Weak transcription	Small Intestine	intestine
33	chr13:30373600-30374800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:30373600-30374800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:30373600-30375200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr13:30373600-30375400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr13:30373600-30375600	Weak transcription	Adipose Nuclei	Adipose
38	chr13:30373600-30376000	Weak transcription	Fetal Thymus	thymus
39	chr13:30373800-30375600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:30374000-30374400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr13:30374000-30374800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:30374000-30380200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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