Variant report

Variant	rs9396214
Chromosome Location	chr6:56342806-56342807
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56340912..56343256-chr6:56347717..56349911,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11753813	0.82[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756977	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs11758339	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11759493	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961668	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12174955	0.85[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12527139	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13204556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359068	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359070	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535610	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535612	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570492	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17825773	0.89[MEX][hapmap]
rs2273972	0.81[CEU][hapmap];0.98[GIH][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273973	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273974	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2397226	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894837	0.88[CHB][hapmap];0.94[MEX][hapmap]
rs34954984	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35671304	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35926142	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927453	0.89[ASN][1000 genomes]
rs4130060	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143828	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4236139	0.81[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs4236140	0.95[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236141	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4236142	0.82[ASN][1000 genomes]
rs4236143	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4236144	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs4236145	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs4283892	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331988	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4346846	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4454141	0.82[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap]
rs4466244	0.82[ASN][1000 genomes]
rs4499917	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4544910	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45486696	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712132	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs4712133	0.87[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap]
rs4715625	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715626	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap]
rs4715627	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs4715628	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs4715629	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap]
rs4715630	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4715631	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs59101638	0.88[ASN][1000 genomes]
rs6459161	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs6459163	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656550	0.82[AMR][1000 genomes]
rs656988	0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs6904202	0.81[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs6906792	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs6907917	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6911502	0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs6913572	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914325	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6919608	0.95[GIH][hapmap]
rs6922770	0.82[CEU][hapmap]
rs6927258	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928601	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6939305	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs721475	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877350	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741295	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7746753	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755220	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755361	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs7755573	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7758054	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759875	0.84[CEU][hapmap]
rs7760640	0.86[CEU][hapmap]
rs7760695	0.82[EUR][1000 genomes]
rs7761281	0.86[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap]
rs7762629	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9296848	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296850	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9349822	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9349823	0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349824	0.89[ASN][1000 genomes]
rs9349825	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349828	0.86[JPT][hapmap]
rs9357921	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9357922	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9370531	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370533	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9370534	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370535	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382631	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382635	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9396211	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396213	0.86[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9396215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396218	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464389	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9475709	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475713	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs9475714	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs9475716	0.82[EUR][1000 genomes];0.81[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:56315000-56349800	Strong transcription	HSMM	muscle
4	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
7	chr6:56319400-56343600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:56319400-56344200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:56321000-56343400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:56321200-56343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:56322200-56349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:56322400-56344200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:56322600-56348200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:56325000-56346600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:56327200-56351400	Weak transcription	Fetal Thymus	thymus
16	chr6:56328600-56362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:56329200-56373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:56330000-56351400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:56330000-56372400	Weak transcription	Lung	lung
20	chr6:56330200-56347200	Weak transcription	Small Intestine	intestine
21	chr6:56330200-56357400	Weak transcription	Esophagus	oesophagus
22	chr6:56332800-56346000	Strong transcription	Adipose Nuclei	Adipose
23	chr6:56332800-56349200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:56333000-56344400	Strong transcription	GM12878-XiMat	blood
25	chr6:56333000-56350000	Strong transcription	HMEC	breast
26	chr6:56333200-56343000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:56333200-56343000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:56334400-56348200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:56334400-56359400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:56336600-56347400	Weak transcription	K562	blood
31	chr6:56337600-56348000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:56337600-56350800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:56337600-56351400	Weak transcription	Aorta	Aorta
34	chr6:56337600-56351400	Weak transcription	Pancreas	Pancrea
35	chr6:56337600-56364600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:56337600-56376000	Weak transcription	Gastric	stomach
37	chr6:56339600-56345600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:56339800-56354400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:56339800-56355800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:56340000-56344400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:56340200-56344400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:56340200-56347800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:56340600-56343400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:56340600-56343600	Strong transcription	Fetal Stomach	stomach
45	chr6:56340800-56346800	Weak transcription	Right Ventricle	heart
46	chr6:56341000-56344200	Genic enhancers	Liver	Liver
47	chr6:56341000-56344200	Weak transcription	Fetal Kidney	kidney
48	chr6:56341000-56346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:56341000-56347000	Weak transcription	Stomach Mucosa	stomach
50	chr6:56341200-56343200	Strong transcription	Fetal Lung	lung

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