Variant report

Variant	rs4399408
Chromosome Location	chr13:30367283-30367284
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	chr13:30343717..30345488-chr13:30365364..30367751,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][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	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1631987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][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[CHD][hapmap];1.00[MEX][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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1747058	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747059	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747060	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1747061	1.00[ASN][1000 genomes]
rs1747062	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][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];0.85[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]
rs2794299	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]
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];0.92[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142339	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142340	1.00[AFR][1000 genomes];0.96[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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs4611301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4769021	0.89[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57634252	1.00[ASN][1000 genomes]
rs58961964	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59768871	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs598281	1.00[TSI][hapmap]
rs6490427	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490428	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490431	1.00[AFR][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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7322158	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73444211	0.89[EUR][1000 genomes]
rs73444214	0.81[AMR][1000 genomes]
rs74042393	0.89[EUR][1000 genomes]
rs74044752	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983788	0.85[AFR][1000 genomes];0.96[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];0.85[YRI][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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs818763	0.82[ASN][1000 genomes]
rs818764	1.00[ASN][1000 genomes]
rs912394	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314977	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs943561	0.82[ASN][1000 genomes]
rs9508549	0.82[ASN][1000 genomes]
rs9508551	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550492	0.85[AFR][1000 genomes];0.96[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];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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
2	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:30360400-30368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:30360600-30368000	Weak transcription	Fetal Intestine Large	intestine
6	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:30361400-30367400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr13:30361800-30373000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:30362400-30370800	Weak transcription	NHDF-Ad	bronchial
10	chr13:30362400-30375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:30362600-30372600	Weak transcription	Small Intestine	intestine
12	chr13:30362800-30368400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr13:30363200-30373200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr13:30363400-30368000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:30363400-30372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:30363400-30375400	Weak transcription	Lung	lung
17	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
18	chr13:30364200-30372200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:30365000-30368200	Enhancers	Brain Anterior Caudate	brain
20	chr13:30365000-30373000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:30365200-30370600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr13:30365400-30368000	Enhancers	Brain Substantia Nigra	brain
23	chr13:30365600-30368400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:30365800-30367600	Enhancers	Brain Germinal Matrix	brain
25	chr13:30365800-30383200	Weak transcription	Ovary	ovary
26	chr13:30366000-30368000	Weak transcription	Pancreas	Pancrea
27	chr13:30366000-30368800	Weak transcription	Liver	Liver
28	chr13:30366000-30375200	Weak transcription	Gastric	stomach
29	chr13:30366000-30375600	Weak transcription	Brain Angular Gyrus	brain
30	chr13:30366200-30367800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
32	chr13:30366600-30367600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:30366600-30369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:30366800-30367600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:30366800-30367600	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:30366800-30367800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr13:30366800-30370400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr13:30366800-30370600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:30367000-30367400	Enhancers	Fetal Brain Male	brain
40	chr13:30367000-30370800	Weak transcription	Osteobl	bone
41	chr13:30367200-30367600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:30367200-30368200	Enhancers	Brain Hippocampus Middle	brain
43	chr13:30367200-30368800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr13:30367200-30368800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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