Variant report

Variant	rs9458859
Chromosome Location	chr6:163983858-163983859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163982012..163984451-chr6:163998369..164000574,2	K562	blood:
2	chr6:163978491..163982172-chr6:163982815..163986185,4	K562	blood:
3	chr6:163835158..163838098-chr6:163983695..163986394,2	MCF-7	breast:
4	chr6:163836144..163840696-chr6:163983068..163987938,4	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10080505	0.94[EUR][1000 genomes]
rs11964059	0.82[MEX][hapmap]
rs12523713	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12523978	0.90[EUR][1000 genomes]
rs17176494	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs4112651	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs60332904	0.82[EUR][1000 genomes]
rs6455905	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6901592	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6902608	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6906081	0.84[EUR][1000 genomes]
rs6906275	0.84[EUR][1000 genomes]
rs6906725	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6910323	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6914093	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6917030	0.84[EUR][1000 genomes]
rs6928869	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6936927	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6937072	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6937097	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs73013516	0.84[EUR][1000 genomes]
rs73013528	0.80[EUR][1000 genomes]
rs73013553	0.84[EUR][1000 genomes]
rs73015316	0.92[EUR][1000 genomes]
rs7748261	0.84[EUR][1000 genomes]
rs7759606	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7761090	0.90[EUR][1000 genomes]
rs7770852	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9456868	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9458821	0.86[EUR][1000 genomes]
rs9458823	0.92[CEU][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9458825	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs9458827	0.94[EUR][1000 genomes]
rs9458828	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9458830	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs9458837	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9458846	0.90[GIH][hapmap]
rs9458849	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9458854	0.90[GIH][hapmap]
rs9458855	0.90[GIH][hapmap]
rs9458857	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9654569	0.92[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:163951600-163985800	Weak transcription	Hela-S3	cervix
6	chr6:163952400-163984400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:163952600-163996600	Weak transcription	Gastric	stomach
8	chr6:163954000-163984200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:163954000-163984400	Weak transcription	Aorta	Aorta
10	chr6:163954000-163991600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:163954800-163984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:163955200-163984200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:163955800-163984400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:163958200-163984600	Weak transcription	HMEC	breast
15	chr6:163958200-163991600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:163958400-163984400	Weak transcription	Fetal Thymus	thymus
17	chr6:163959600-163984400	Weak transcription	Ovary	ovary
18	chr6:163959800-163997200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:163960400-163984400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:163960600-163993000	Weak transcription	A549	lung
21	chr6:163961600-163984800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:163965400-163984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:163965600-163995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:163966800-163984400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:163966800-163987000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:163967200-163984200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:163968800-163991800	Weak transcription	Fetal Brain Male	brain
28	chr6:163969000-163991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:163970400-163991600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:163970800-164000200	Weak transcription	Right Atrium	heart
31	chr6:163972200-163984400	Strong transcription	HSMM	muscle
32	chr6:163972600-163995600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:163974000-163997000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:163974200-163997000	Weak transcription	Fetal Intestine Large	intestine
35	chr6:163975400-163984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:163976000-163993200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:163977000-163993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:163978000-163998000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:163978200-163984400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:163978400-163989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:163978800-163997600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:163979200-163985800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:163979200-163996200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:163979400-163987600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:163979400-163989200	Strong transcription	HepG2	liver
46	chr6:163979800-163989200	Genic enhancers	Brain Substantia Nigra	brain
47	chr6:163979800-163990600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:163980000-163984400	Weak transcription	Fetal Stomach	stomach
49	chr6:163980000-163984400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:163980000-163984400	Weak transcription	Spleen	Spleen

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