Variant report

Variant	rs12209889
Chromosome Location	chr6:144936035-144936036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144934417..144936972-chr6:144942028..144944059,3	MCF-7	breast:
2	chr6:144933907..144936747-chr6:144940760..144942377,2	K562	blood:
3	chr6:144924091..144927030-chr6:144935405..144937904,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10080939	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10447422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10457761	0.86[CHB][hapmap]
rs10457764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10499230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11155359	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11155367	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11155369	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11756963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12190718	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12192622	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12198720	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs12200263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202537	0.86[CEU][hapmap]
rs12202539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12204734	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12205460	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12209699	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17073869	0.86[EUR][1000 genomes]
rs17793570	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1918749	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28588721	0.81[EUR][1000 genomes]
rs34810766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259269	0.92[CEU][hapmap]
rs4460225	0.86[EUR][1000 genomes]
rs4615409	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56264877	0.86[EUR][1000 genomes]
rs60530618	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570634	0.85[CHB][hapmap]
rs6570641	1.00[YRI][hapmap]
rs6912724	0.85[CHB][hapmap]
rs6917268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6917519	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923281	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942069	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73600166	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73600170	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73603015	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321976	0.86[CHB][hapmap]
rs9497026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs951572	0.84[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144881800-144937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:144885800-144943400	Weak transcription	Ovary	ovary
3	chr6:144904600-144939800	Weak transcription	HSMMtube	muscle
4	chr6:144908800-144947400	Weak transcription	HUVEC	blood vessel
5	chr6:144914800-144937800	Weak transcription	HSMM	muscle
6	chr6:144914800-144960000	Weak transcription	Lung	lung
7	chr6:144922200-144938400	Weak transcription	Liver	Liver
8	chr6:144922600-144938600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:144922800-144939000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:144923000-144938000	Weak transcription	NHDF-Ad	bronchial
11	chr6:144929600-144955200	Weak transcription	HepG2	liver
12	chr6:144929800-144938400	Weak transcription	Adipose Nuclei	Adipose
13	chr6:144929800-144945600	Weak transcription	Left Ventricle	heart
14	chr6:144930000-144943800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:144930000-144945600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:144930000-144950200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:144930200-144938000	Weak transcription	Fetal Heart	heart
18	chr6:144930200-144940800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:144930400-144957600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:144930600-144973000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:144930800-144951800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:144930800-144957800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:144931000-144958800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:144932200-144936200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:144932200-144937200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:144932400-144936800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:144932600-144936200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:144932600-144937400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr6:144932600-144938000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:144934000-144936200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:144934000-144938200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:144934200-144937000	Strong transcription	Primary B cells from cord blood	blood
33	chr6:144934200-144938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:144934400-144941800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:144936000-144938200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:144936000-144941000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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