Variant report

Variant	rs9458821
Chromosome Location	chr6:163828063-163828064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163825837..163828170-chr6:163829514..163831485,3	MCF-7	breast:
2	chr6:163824877..163830472-chr6:163836413..163839637,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10080505	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523713	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12523978	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17176494	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4112651	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60332904	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6455905	0.86[EUR][1000 genomes]
rs6901592	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6902608	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6905884	0.81[EUR][1000 genomes]
rs6906081	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6906275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6906725	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6910323	0.92[EUR][1000 genomes]
rs6914093	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6917030	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6928869	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6936927	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6937072	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6937097	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73013516	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73013528	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73013553	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73015316	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7748261	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7759606	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7761090	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770852	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9456868	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458823	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458825	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458827	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458828	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458830	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458837	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458849	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458857	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458859	0.86[EUR][1000 genomes]
rs9654569	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1791729	chr6:163814557-163836689	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1839403	chr6:163822296-163835490	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1793461	chr6:163822296-163836634	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1794611	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1796475	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1797016	chr6:163822296-163836689	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1801202	chr6:163822296-163836689	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1801861	chr6:163822296-163836689	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv605193	chr6:163824864-163835490	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv605194	chr6:163824864-163836293	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv605195	chr6:163824864-163836634	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163825200-163828200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:163827000-163832000	Weak transcription	Gastric	stomach
3	chr6:163827200-163830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:163827200-163832000	Weak transcription	Placenta	Placenta
5	chr6:163827200-163832000	Weak transcription	Lung	lung
6	chr6:163827200-163833600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:163827200-163833600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:163827200-163833800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:163827200-163834200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:163827200-163834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:163827200-163834200	Weak transcription	Spleen	Spleen
12	chr6:163827400-163828200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:163827400-163828200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:163827400-163828200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:163827400-163828200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:163827400-163828200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:163827400-163828200	Enhancers	Fetal Brain Female	brain
18	chr6:163827400-163828200	Enhancers	Fetal Muscle Leg	muscle
19	chr6:163827400-163828800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:163827400-163829000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:163827400-163829600	Weak transcription	A549	lung
22	chr6:163827400-163830400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:163827400-163830800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:163827400-163832400	Weak transcription	Left Ventricle	heart
25	chr6:163827400-163833000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:163827400-163833400	Weak transcription	HSMM	muscle
27	chr6:163827400-163833600	Weak transcription	Psoas Muscle	Psoas
28	chr6:163827400-163833600	Weak transcription	Right Atrium	heart
29	chr6:163827400-163833800	Weak transcription	Aorta	Aorta
30	chr6:163827600-163828200	Enhancers	Primary B cells from cord blood	blood
31	chr6:163827600-163828200	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:163827600-163828200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:163827600-163828200	Enhancers	Liver	Liver
34	chr6:163827600-163828200	Enhancers	Brain Germinal Matrix	brain
35	chr6:163827600-163828200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:163827600-163828200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:163827600-163828400	Enhancers	Brain Substantia Nigra	brain
38	chr6:163827600-163828600	Enhancers	Adipose Nuclei	Adipose
39	chr6:163827600-163828800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:163827600-163828800	Enhancers	Brain Angular Gyrus	brain
41	chr6:163827600-163828800	Enhancers	Brain Hippocampus Middle	brain
42	chr6:163827600-163828800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:163827600-163828800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:163827600-163828800	Enhancers	NHDF-Ad	bronchial
45	chr6:163827600-163829000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:163827600-163829200	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:163827600-163829600	Enhancers	HepG2	liver
48	chr6:163827600-163832000	Weak transcription	HSMMtube	muscle
49	chr6:163827600-163833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:163827600-163833400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links