Variant report

Variant	rs4886825
Chromosome Location	chr15:76971456-76971457
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	chr15:76964455..76968844-chr15:76969640..76972722,4	K562	blood:
2	chr15:76969596..76972550-chr15:76979737..76981959,2	MCF-7	breast:

Extended variants
information (count: 161 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10444858	0.99[ASN][1000 genomes]
rs11072599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11072603	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1116535	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1117367	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1125932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12148452	1.00[ASN][1000 genomes]
rs12148786	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12148805	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12148877	0.86[ASN][1000 genomes]
rs12437627	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12437733	0.84[ASN][1000 genomes]
rs12438077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12438186	0.86[ASN][1000 genomes]
rs12438540	0.87[ASN][1000 genomes]
rs12440151	0.86[ASN][1000 genomes]
rs12440835	0.90[ASN][1000 genomes]
rs12441247	0.84[ASN][1000 genomes]
rs12441433	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12441484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12441550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12443137	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12591660	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12593871	0.89[ASN][1000 genomes]
rs12594556	0.83[ASN][1000 genomes]
rs12594577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12595313	1.00[ASN][1000 genomes]
rs12898430	0.82[ASN][1000 genomes]
rs12900494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12902174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12902452	0.86[ASN][1000 genomes]
rs12903553	0.80[ASN][1000 genomes]
rs12904198	0.84[ASN][1000 genomes]
rs12908421	0.88[ASN][1000 genomes]
rs12910293	0.84[ASN][1000 genomes]
rs12910382	0.89[ASN][1000 genomes]
rs12910734	0.84[ASN][1000 genomes]
rs12911174	0.84[ASN][1000 genomes]
rs12911902	0.89[ASN][1000 genomes]
rs12911987	0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12916573	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes]
rs12916869	0.82[ASN][1000 genomes]
rs1471780	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17367297	0.83[ASN][1000 genomes]
rs1838048	0.87[ASN][1000 genomes]
rs1867197	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1874944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1946650	0.89[ASN][1000 genomes]
rs2083762	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2120107	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2120108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2137307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2304920	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2404602	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2404733	0.93[ASN][1000 genomes]
rs2404736	0.90[ASN][1000 genomes]
rs2404737	0.90[ASN][1000 genomes]
rs2404740	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2896954	0.81[ASN][1000 genomes]
rs3110382	0.82[ASN][1000 genomes]
rs34049670	0.84[ASN][1000 genomes]
rs34060246	1.00[ASN][1000 genomes]
rs34181263	0.86[ASN][1000 genomes]
rs34272342	0.97[ASN][1000 genomes]
rs34287706	0.87[ASN][1000 genomes]
rs34478400	0.86[ASN][1000 genomes]
rs34639578	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34707035	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924128	1.00[ASN][1000 genomes]
rs35077207	0.87[ASN][1000 genomes]
rs35138393	1.00[ASN][1000 genomes]
rs35170561	0.84[ASN][1000 genomes]
rs35195096	0.87[ASN][1000 genomes]
rs35395069	1.00[ASN][1000 genomes]
rs35498563	1.00[ASN][1000 genomes]
rs35557205	0.83[ASN][1000 genomes]
rs35561811	0.84[ASN][1000 genomes]
rs35566346	0.86[ASN][1000 genomes]
rs36070630	0.93[ASN][1000 genomes]
rs3816266	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4383105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4442773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4525456	0.86[ASN][1000 genomes]
rs4641709	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4886496	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4886503	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4886813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4886817	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4886818	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4886822	0.86[ASN][1000 genomes]
rs4886824	0.98[ASN][1000 genomes]
rs4886829	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs55676827	1.00[ASN][1000 genomes]
rs55864032	0.84[ASN][1000 genomes]
rs56193230	0.87[ASN][1000 genomes]
rs56351018	0.84[ASN][1000 genomes]
rs57178708	0.86[ASN][1000 genomes]
rs58361452	1.00[ASN][1000 genomes]
rs58511211	0.84[ASN][1000 genomes]
rs58973160	1.00[ASN][1000 genomes]
rs59088060	0.89[ASN][1000 genomes]
rs60658665	0.90[ASN][1000 genomes]
rs60912217	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495206	0.82[ASN][1000 genomes]
rs66754747	0.84[ASN][1000 genomes]
rs66866130	0.84[ASN][1000 genomes]
rs67010831	1.00[ASN][1000 genomes]
rs67204011	0.89[ASN][1000 genomes]
rs67570291	1.00[ASN][1000 genomes]
rs71405216	0.86[ASN][1000 genomes]
rs71405222	0.95[ASN][1000 genomes]
rs71405223	1.00[ASN][1000 genomes]
rs71405225	0.85[ASN][1000 genomes]
rs7163397	0.87[ASN][1000 genomes]
rs7167613	0.84[ASN][1000 genomes]
rs7169394	0.86[ASN][1000 genomes]
rs7174673	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7174953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs72738889	1.00[ASN][1000 genomes]
rs7342603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7350777	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7495566	0.92[ASN][1000 genomes]
rs8024476	1.00[ASN][1000 genomes]
rs8028294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8036703	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8037005	0.93[ASN][1000 genomes]
rs8040539	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs8043474	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9646213	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
15	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
16	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv570023	chr15:76884127-76978139	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
24	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv570109	chr15:76907376-76978139	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv904413	chr15:76923917-76995150	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv457206	chr15:76971456-77121196	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv570110	chr15:76971456-77121196	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4886825	C15orf17	cis	parietal	SCAN
rs4886825	NRG4	cis	parietal	SCAN
rs4886825	ODF3L1	cis	parietal	SCAN
rs4886825	SCAPER	cis	cerebellum	SCAN
rs4886825	SCAPER	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76898400-76981000	Weak transcription	Pancreas	Pancrea
3	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76911400-76990800	Weak transcription	Placenta	Placenta
5	chr15:76926600-76974600	Weak transcription	Esophagus	oesophagus
6	chr15:76933200-76974800	Weak transcription	Thymus	Thymus
7	chr15:76936600-76991800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:76940200-76991800	Weak transcription	Left Ventricle	heart
9	chr15:76941400-76991600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:76941800-76974200	Weak transcription	Fetal Stomach	stomach
11	chr15:76941800-76976200	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:76942400-76991800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:76944600-76973800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:76947400-76991600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:76947400-76991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:76952000-76974600	Weak transcription	Right Ventricle	heart
17	chr15:76952800-76972200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:76952800-76972800	Weak transcription	Primary B cells from cord blood	blood
19	chr15:76954200-76992000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:76956200-76975800	Weak transcription	Fetal Intestine Large	intestine
21	chr15:76957600-76991600	Weak transcription	Liver	Liver
22	chr15:76957800-76991200	Weak transcription	Primary T cells from cord blood	blood
23	chr15:76958000-76974600	Weak transcription	Adipose Nuclei	Adipose
24	chr15:76958200-76973800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:76961200-76992000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:76970600-76971800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:76970800-76971600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:76970800-76971600	Enhancers	NHDF-Ad	bronchial
29	chr15:76970800-76971800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr15:76971000-76971800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:76971000-76971800	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links