Variant report

Variant	rs9390180
Chromosome Location	chr6:144943157-144943158
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	chr6:144934417..144936972-chr6:144942028..144944059,3	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1005974	0.86[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs10434891	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11155357	0.82[ASN][1000 genomes]
rs11155361	0.91[EUR][1000 genomes]
rs12204372	0.80[ASN][1000 genomes]
rs12214126	0.82[ASN][1000 genomes]
rs13191597	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs13193448	0.81[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13195928	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs13198102	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13201946	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13203229	0.81[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs13203387	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13205040	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13207026	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13218121	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1534437	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1554814	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1554816	0.90[CHD][hapmap];0.86[GIH][hapmap]
rs1590055	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17793810	0.81[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1830271	0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1918744	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1918745	0.94[EUR][1000 genomes]
rs1918746	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs1918747	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs1918748	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs2178128	0.81[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34053805	0.94[EUR][1000 genomes]
rs34504312	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34571592	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35161160	0.94[EUR][1000 genomes]
rs35524567	0.95[EUR][1000 genomes]
rs35904953	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811099	0.93[JPT][hapmap]
rs3924656	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3924657	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4052725	0.90[EUR][1000 genomes]
rs4146297	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs4401687	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs4438980	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs4568467	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4582403	0.91[EUR][1000 genomes]
rs56039703	0.94[EUR][1000 genomes]
rs56158631	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56185703	0.83[ASN][1000 genomes]
rs67767204	0.94[EUR][1000 genomes]
rs6908795	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs6915390	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs6918394	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs6919793	0.94[EUR][1000 genomes]
rs6920388	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs6924812	0.94[EUR][1000 genomes]
rs6938409	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs6938455	0.91[EUR][1000 genomes]
rs6938776	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73001731	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73005504	0.94[EUR][1000 genomes]
rs73005509	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73005511	0.94[EUR][1000 genomes]
rs7740593	0.80[ASN][1000 genomes]
rs7753246	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs9376829	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376830	0.94[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes]
rs9390177	0.81[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs9390179	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9390181	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390185	0.82[ASW][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs9403565	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403566	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403569	0.81[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs9403570	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403571	0.94[CEU][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9497023	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952050	0.81[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs952051	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[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	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144885800-144943400	Weak transcription	Ovary	ovary
2	chr6:144908800-144947400	Weak transcription	HUVEC	blood vessel
3	chr6:144914800-144960000	Weak transcription	Lung	lung
4	chr6:144929600-144955200	Weak transcription	HepG2	liver
5	chr6:144929800-144945600	Weak transcription	Left Ventricle	heart
6	chr6:144930000-144943800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:144930000-144945600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:144930000-144950200	Weak transcription	Primary T cells from cord blood	blood
9	chr6:144930400-144957600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:144930600-144973000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:144930800-144951800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:144930800-144957800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:144931000-144958800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:144939000-144945600	Weak transcription	Pancreas	Pancrea
15	chr6:144939000-144949800	Weak transcription	Primary B cells from cord blood	blood
16	chr6:144939000-144959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:144939200-144945800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:144939400-144949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:144940600-144945800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:144941200-144945200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:144941200-144947200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:144941400-144944000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:144941400-144945400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:144941400-144951800	Weak transcription	Fetal Heart	heart
25	chr6:144942400-144943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:144943000-144947600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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