Variant report

Variant	rs9263499
Chromosome Location	chr6:31064710-31064711
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	chr6:30710595..30712129-chr6:31063748..31065436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10947134	0.83[ASN][1000 genomes]
rs10947135	0.85[ASN][1000 genomes]
rs12527394	0.94[ASN][1000 genomes]
rs12529288	0.98[ASN][1000 genomes]
rs12662091	0.85[ASN][1000 genomes]
rs2233964	0.85[EUR][1000 genomes]
rs2233965	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2233970	0.85[ASN][1000 genomes]
rs2233973	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2233983	0.85[ASN][1000 genomes]
rs2233984	0.85[ASN][1000 genomes]
rs2233985	0.85[ASN][1000 genomes]
rs2394416	0.82[EUR][1000 genomes]
rs2394419	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2517473	0.85[ASN][1000 genomes]
rs2894179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34209658	0.97[ASN][1000 genomes]
rs35802713	0.97[ASN][1000 genomes]
rs3734854	0.85[ASN][1000 genomes]
rs4486065	0.87[EUR][1000 genomes]
rs4495304	0.82[ASN][1000 genomes]
rs4713431	0.94[ASN][1000 genomes]
rs4947246	0.89[ASN][1000 genomes]
rs4947296	0.98[ASN][1000 genomes]
rs4947297	0.97[ASN][1000 genomes]
rs4947299	0.93[ASN][1000 genomes]
rs4947302	0.89[ASN][1000 genomes]
rs9263460	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9263477	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9263508	0.84[EUR][1000 genomes]
rs9263509	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9263512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9263560	0.81[EUR][1000 genomes]
rs9263572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9263578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295949	0.94[ASN][1000 genomes]
rs9295950	0.94[ASN][1000 genomes]
rs9295951	0.81[EUR][1000 genomes]
rs9348854	0.97[ASN][1000 genomes]
rs9357108	0.97[ASN][1000 genomes]
rs9380215	0.94[ASN][1000 genomes]
rs9380217	0.94[ASN][1000 genomes]
rs9391708	0.89[ASN][1000 genomes]
rs9391709	0.85[ASN][1000 genomes]
rs9394037	0.97[ASN][1000 genomes]
rs9394038	0.97[ASN][1000 genomes]
rs9405049	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31058800-31066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:31060600-31065200	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:31060800-31066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:31061000-31065800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:31061200-31064800	Weak transcription	K562	blood
6	chr6:31061600-31065600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:31061600-31065600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:31061800-31066000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:31062000-31065200	Enhancers	Spleen	Spleen
10	chr6:31062600-31065800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:31062600-31066600	Enhancers	HUVEC	blood vessel
12	chr6:31062800-31065400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:31062800-31065600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:31062800-31065800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:31062800-31066000	Weak transcription	Lung	lung
16	chr6:31062800-31070000	Weak transcription	A549	lung
17	chr6:31063000-31065800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:31063000-31065800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:31063000-31065800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:31063200-31064800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:31063200-31065600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr6:31063200-31065600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:31063200-31070000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:31063200-31070000	Weak transcription	HMEC	breast
25	chr6:31063600-31064800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:31064200-31065000	Enhancers	Brain Germinal Matrix	brain
27	chr6:31064400-31065000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:31064600-31064800	Enhancers	Adipose Nuclei	Adipose
29	chr6:31064600-31065000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:31064600-31065400	Enhancers	Duodenum Mucosa	Duodenum
31	chr6:31064600-31065600	Enhancers	HepG2	liver

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