Variant report

Variant	rs2794299
Chromosome Location	chr13:30392819-30392820
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	chr13:30391873..30393700-chr13:30497127..30499566,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1099277	1.00[ASN][1000 genomes]
rs12861019	1.00[ASN][1000 genomes]
rs12864739	1.00[ASN][1000 genomes]
rs12865525	1.00[ASN][1000 genomes]
rs12867537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12868298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12869833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12872768	1.00[ASN][1000 genomes]
rs12874615	1.00[ASN][1000 genomes]
rs12875231	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12877107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1327643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1571255	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1631987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17073897	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17073905	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17073919	1.00[ASN][1000 genomes]
rs1747057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747058	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747059	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747061	1.00[ASN][1000 genomes]
rs1747062	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747063	1.00[ASN][1000 genomes]
rs17502757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1772726	1.00[ASN][1000 genomes]
rs2009535	0.82[ASN][1000 genomes]
rs2031280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs2182775	0.82[ASN][1000 genomes]
rs2182776	0.82[ASN][1000 genomes]
rs2182777	0.82[ASN][1000 genomes]
rs2182778	0.89[EUR][1000 genomes]
rs2256122	1.00[ASN][1000 genomes]
rs2476650	1.00[ASN][1000 genomes]
rs2476651	1.00[ASN][1000 genomes]
rs2761929	1.00[ASN][1000 genomes]
rs2761930	1.00[ASN][1000 genomes]
rs2761931	1.00[ASN][1000 genomes]
rs2761932	1.00[ASN][1000 genomes]
rs2761934	1.00[ASN][1000 genomes]
rs2761936	1.00[ASN][1000 genomes]
rs278031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278032	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278039	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278043	1.00[ASN][1000 genomes]
rs278047	1.00[ASN][1000 genomes]
rs2794295	1.00[ASN][1000 genomes]
rs2794296	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2794300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118079	0.87[ASN][1000 genomes]
rs3118080	1.00[ASN][1000 genomes]
rs34232669	1.00[ASN][1000 genomes]
rs34333613	0.93[ASN][1000 genomes]
rs35693706	1.00[ASN][1000 genomes]
rs35828457	1.00[ASN][1000 genomes]
rs36082926	1.00[ASN][1000 genomes]
rs4083609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142340	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335642	0.87[ASN][1000 genomes]
rs4379924	0.87[ASN][1000 genomes]
rs4385989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs4399408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4769021	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4769023	0.82[ASN][1000 genomes]
rs4769024	1.00[ASN][1000 genomes]
rs4769773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57634252	1.00[ASN][1000 genomes]
rs58961964	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59768871	0.89[EUR][1000 genomes]
rs6490427	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490428	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490431	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71427282	1.00[ASN][1000 genomes]
rs71427283	1.00[ASN][1000 genomes]
rs71434758	1.00[ASN][1000 genomes]
rs719199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7322158	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73444211	0.89[EUR][1000 genomes]
rs74042393	0.89[EUR][1000 genomes]
rs74044752	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983788	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985986	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7992684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8000607	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8001320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001330	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs818763	0.82[ASN][1000 genomes]
rs818764	1.00[ASN][1000 genomes]
rs912394	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs943561	0.82[ASN][1000 genomes]
rs9508549	0.82[ASN][1000 genomes]
rs9508551	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550492	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9551734	0.87[ASN][1000 genomes]
rs968612	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9788356	1.00[EUR][1000 genomes];0.87[ASN][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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30376600-30420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:30385800-30403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:30385800-30406800	Weak transcription	Pancreas	Pancrea
4	chr13:30385800-30410600	Weak transcription	Small Intestine	intestine
5	chr13:30386000-30406200	Weak transcription	Fetal Intestine Small	intestine
6	chr13:30386800-30394000	Weak transcription	Stomach Mucosa	stomach
7	chr13:30387600-30393600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:30389000-30395800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:30389200-30393600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr13:30389800-30394200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:30390400-30394400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr13:30390600-30393600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:30390600-30393800	Enhancers	Primary T cells from cord blood	blood
14	chr13:30390600-30394200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr13:30390600-30394400	Enhancers	Primary B cells from peripheral blood	blood
16	chr13:30390600-30394600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr13:30390800-30393200	Enhancers	Brain Hippocampus Middle	brain
18	chr13:30390800-30394000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr13:30391000-30393200	Enhancers	Brain Anterior Caudate	brain
20	chr13:30391000-30393800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:30391000-30393800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:30391000-30393800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr13:30391000-30394400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr13:30391200-30393000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:30391200-30393000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr13:30391200-30393000	Enhancers	Brain Angular Gyrus	brain
27	chr13:30391200-30393000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr13:30391200-30393200	Enhancers	Duodenum Mucosa	Duodenum
29	chr13:30391200-30393400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr13:30391200-30393600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr13:30391200-30393600	Enhancers	Liver	Liver
32	chr13:30391200-30393800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr13:30391200-30393800	Enhancers	Colon Smooth Muscle	Colon
34	chr13:30391200-30394000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr13:30391200-30410600	Weak transcription	Ovary	ovary
36	chr13:30391400-30393000	Enhancers	Adipose Nuclei	Adipose
37	chr13:30391400-30393200	Enhancers	HSMM	muscle
38	chr13:30391400-30393600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr13:30391400-30393600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:30391400-30393800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr13:30391600-30393000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr13:30391600-30393200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr13:30391600-30393600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr13:30391800-30393000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr13:30391800-30393000	Enhancers	Fetal Kidney	kidney
46	chr13:30391800-30393000	Enhancers	Fetal Lung	lung
47	chr13:30391800-30393200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:30391800-30393600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr13:30392000-30393400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:30392000-30393600	Enhancers	Brain Substantia Nigra	brain

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