Variant report

Variant	rs16915389
Chromosome Location	chr8:87552426-87552427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:87551482-87552440	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:87551519..87555405-chr8:87558017..87562987,4	MCF-7	breast:

Variant related genes	Relation type
CPNE3	TF binding region
ENSG00000085719	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10086188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10089253	0.84[ASN][1000 genomes]
rs10090898	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10090963	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092168	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10094332	1.00[ASN][1000 genomes]
rs10095589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097866	0.84[ASN][1000 genomes]
rs10098365	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100182	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100247	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100254	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10100368	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10106390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10108586	0.84[ASN][1000 genomes]
rs10110096	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10481195	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11774499	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776698	0.84[ASN][1000 genomes]
rs11783382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11984519	0.90[ASN][1000 genomes]
rs11986423	0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs11994508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11997927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11998558	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12155981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs16915375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17681534	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28397606	0.90[ASN][1000 genomes]
rs28416254	0.90[ASN][1000 genomes]
rs28438974	1.00[ASN][1000 genomes]
rs28514445	1.00[ASN][1000 genomes]
rs28540009	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613262	1.00[ASN][1000 genomes]
rs28687116	1.00[ASN][1000 genomes]
rs3087641	1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[ASN][1000 genomes]
rs4440616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs57638937	0.82[ASN][1000 genomes]
rs58837061	0.84[ASN][1000 genomes]
rs6651177	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651268	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67332431	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6980476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6992624	0.90[ASN][1000 genomes]
rs7015772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7018083	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72690416	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72690443	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690447	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690457	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690474	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73688856	0.84[ASN][1000 genomes]
rs73688857	0.88[ASN][1000 genomes]
rs73688858	0.88[ASN][1000 genomes]
rs73688859	0.81[ASN][1000 genomes]
rs73688862	0.88[ASN][1000 genomes]
rs7818436	0.90[ASN][1000 genomes]
rs7823951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7824873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7833201	0.97[ASN][1000 genomes]
rs7843399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7844014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297913	0.90[ASN][1000 genomes]
rs9650128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16915389	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs16915389	CPNE3	cis	cerebellum	SCAN
rs16915389	CPNE3	cis	parietal	SCAN
rs16915389	FAM82B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87527400-87568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87527600-87562000	Weak transcription	Pancreas	Pancrea
3	chr8:87527600-87568200	Weak transcription	Gastric	stomach
4	chr8:87527600-87584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:87527800-87560000	Weak transcription	HSMMtube	muscle
6	chr8:87528000-87563800	Weak transcription	Hela-S3	cervix
7	chr8:87528000-87573600	Weak transcription	Stomach Mucosa	stomach
8	chr8:87528200-87572000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:87528400-87560400	Weak transcription	Thymus	Thymus
10	chr8:87528600-87557200	Weak transcription	Small Intestine	intestine
11	chr8:87528600-87566000	Weak transcription	Spleen	Spleen
12	chr8:87536000-87559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr8:87536600-87556600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:87539400-87554000	Strong transcription	Fetal Intestine Large	intestine
15	chr8:87539600-87560200	Weak transcription	Lung	lung
16	chr8:87540400-87554800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr8:87541200-87554800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr8:87541400-87554800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:87541600-87553000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr8:87541600-87563800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr8:87541600-87570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr8:87542000-87558800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr8:87542400-87553000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:87542600-87554400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:87543000-87553600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr8:87543200-87555000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:87543200-87571200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr8:87543200-87572600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:87543400-87554800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr8:87543400-87568800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:87543600-87554600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr8:87543800-87560000	Weak transcription	Esophagus	oesophagus
33	chr8:87544000-87557000	Weak transcription	Colonic Mucosa	Colon
34	chr8:87544200-87553400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr8:87544200-87557000	Weak transcription	NHLF	lung
36	chr8:87544800-87555400	Weak transcription	GM12878-XiMat	blood
37	chr8:87545000-87554000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr8:87545000-87571400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr8:87545000-87576800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr8:87545200-87556800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:87546400-87569400	Strong transcription	NHDF-Ad	bronchial
42	chr8:87546600-87557200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr8:87546600-87557200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:87546600-87570200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr8:87546600-87570800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:87547400-87554800	Strong transcription	Placenta	Placenta
47	chr8:87547800-87552800	Strong transcription	Liver	Liver
48	chr8:87547800-87563200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:87548000-87553800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:87548400-87554600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links