Variant report

Variant	rs10851850
Chromosome Location	chr15:72486509-72486510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72484916..72487444-chr15:72490191..72493716,4	MCF-7	breast:
2	chr15:72485044..72488486-chr15:72520625..72523876,6	MCF-7	breast:
3	chr15:72484816..72489111-chr15:72521467..72525337,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1000281	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1035744	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072349	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11072350	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630170	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11630611	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11631650	0.84[EUR][1000 genomes]
rs11633028	1.00[ASW][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs11633327	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634608	0.82[EUR][1000 genomes]
rs11634622	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637611	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639282	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442886	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591338	0.83[CEU][hapmap]
rs12592044	0.82[TSI][hapmap]
rs12904652	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs13858	0.84[CEU][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1481862	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16956623	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16956634	0.83[CEU][hapmap]
rs2034879	0.94[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs2052713	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278987	0.88[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2415134	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899776	0.80[EUR][1000 genomes]
rs2912231	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2929508	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2929509	0.80[EUR][1000 genomes]
rs2929511	0.81[EUR][1000 genomes]
rs2929517	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2929518	0.89[CEU][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs2929532	0.85[EUR][1000 genomes]
rs2957361	0.85[EUR][1000 genomes]
rs2957365	0.86[EUR][1000 genomes]
rs2957373	0.83[CEU][hapmap]
rs2957724	0.81[EUR][1000 genomes]
rs2957734	0.82[EUR][1000 genomes]
rs2957735	0.81[EUR][1000 genomes]
rs2957736	0.81[EUR][1000 genomes]
rs2957740	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2957742	0.81[EUR][1000 genomes]
rs2957745	0.81[EUR][1000 genomes]
rs2957750	0.84[EUR][1000 genomes]
rs35603965	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759820	0.82[EUR][1000 genomes]
rs3759900	0.83[CEU][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3759902	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4454922	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4506844	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55679065	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55763892	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56103540	0.82[AFR][1000 genomes]
rs59975112	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62022788	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62022789	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494992	0.88[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6494997	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs713048	0.89[CEU][hapmap]
rs7162299	0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[EUR][1000 genomes]
rs7164780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7169264	0.82[EUR][1000 genomes]
rs7170456	0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7175197	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175792	0.89[CEU][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7179427	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179942	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182776	0.82[TSI][hapmap]
rs7183055	0.87[EUR][1000 genomes]
rs7183196	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7183810	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72733339	0.82[AFR][1000 genomes]
rs8023788	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8025939	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8027164	0.89[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs8027647	0.93[EUR][1000 genomes]
rs8028115	0.89[CEU][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs8030815	0.89[CEU][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032222	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037381	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8038007	0.93[EUR][1000 genomes]
rs8040216	0.82[EUR][1000 genomes]
rs8040828	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8192362	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8192386	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs8192431	0.83[CEU][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10851850	SENP8	cis	cerebellum	SCAN
rs10851850	PARP6	cis	parietal	SCAN
rs10851850	TIPIN	cis	parietal	SCAN
rs10851850	AAGAB	cis	cerebellum	SCAN
rs10851850	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72477000-72487800	Weak transcription	Esophagus	oesophagus
2	chr15:72477000-72489400	Weak transcription	Right Atrium	heart
3	chr15:72480400-72487400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:72483400-72489000	Weak transcription	Fetal Intestine Small	intestine
5	chr15:72485000-72487400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:72485200-72487200	Weak transcription	NHEK	skin
7	chr15:72485200-72487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:72485200-72489000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:72485200-72489000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:72485200-72489000	Enhancers	Placenta	Placenta
11	chr15:72485200-72489200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:72485200-72490400	Weak transcription	A549	lung
13	chr15:72485200-72490400	Weak transcription	HSMM	muscle
14	chr15:72485400-72487200	Weak transcription	HMEC	breast
15	chr15:72485600-72489000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:72486200-72486600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr15:72486200-72486600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr15:72486200-72486600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:72486200-72486600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:72486200-72486800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr15:72486400-72486600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr15:72486400-72486600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr15:72486400-72486600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:72486400-72487000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links