Variant report

Variant	rs16899660
Chromosome Location	chr8:125534041-125534042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125528338..125530863-chr8:125530890..125534338,3	MCF-7	breast:
2	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
3	chr8:125485539..125488439-chr8:125531952..125535064,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTSS1-3	chr8:125533878-125534441	NONHSAT128593

Variant related genes	Relation type
ENSG00000170881	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10107762	1.00[ASW][hapmap]
rs10195	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10956186	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13251109	1.00[ASW][hapmap]
rs13253319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16899643	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298171	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3812470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829033	0.89[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829037	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3857946	1.00[ASW][hapmap]
rs4007921	1.00[ASW][hapmap]
rs4330675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4613980	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4621790	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57929284	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6989097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017148	0.88[ASN][1000 genomes]
rs71516748	0.97[ASN][1000 genomes]
rs72713019	0.92[EUR][1000 genomes]
rs72713023	0.85[EUR][1000 genomes]
rs72713032	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713042	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713045	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713053	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72713055	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713059	0.86[EUR][1000 genomes]
rs72713071	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713073	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713075	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713077	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713084	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713096	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72713098	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72714708	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73704274	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9643197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:125489000-125541200	Weak transcription	Gastric	stomach
3	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
4	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:125499000-125537200	Weak transcription	Esophagus	oesophagus
8	chr8:125500000-125538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:125500000-125538400	Weak transcription	Psoas Muscle	Psoas
10	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
11	chr8:125501600-125535000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
14	chr8:125505800-125538600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr8:125506000-125538600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr8:125510200-125536800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:125510400-125536200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:125511600-125536400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:125512000-125536000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:125512400-125535800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr8:125512400-125536400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr8:125512600-125535600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr8:125512800-125535600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr8:125513200-125535800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:125516200-125537200	Weak transcription	Lung	lung
26	chr8:125516200-125543600	Weak transcription	Aorta	Aorta
27	chr8:125516200-125549600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr8:125516200-125549600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:125516400-125549600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr8:125519200-125550000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:125521600-125535000	Weak transcription	Brain Angular Gyrus	brain
33	chr8:125521800-125535400	Weak transcription	Brain Anterior Caudate	brain
34	chr8:125523000-125536800	Weak transcription	Stomach Mucosa	stomach
35	chr8:125525200-125535000	Weak transcription	Brain Substantia Nigra	brain
36	chr8:125525200-125549600	Weak transcription	Brain Germinal Matrix	brain
37	chr8:125525400-125535800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr8:125525400-125536200	Weak transcription	Ovary	ovary
39	chr8:125526600-125535000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:125526600-125536800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr8:125526600-125541000	Weak transcription	Colonic Mucosa	Colon
42	chr8:125526800-125537200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr8:125527200-125537000	Weak transcription	Pancreas	Pancrea
44	chr8:125527200-125539600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr8:125527400-125535000	Weak transcription	Thymus	Thymus
46	chr8:125527400-125535400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr8:125527400-125541000	Weak transcription	Fetal Heart	heart
48	chr8:125527600-125535000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr8:125527600-125537600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:125527600-125550200	Weak transcription	Fetal Brain Female	brain

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