Variant report

Variant	rs8028660
Chromosome Location	chr15:41156120-41156121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41154663..41156946-chr15:41157971..41160797,2	K562	blood:
2	chr15:41135972..41139917-chr15:41154366..41159199,4	K562	blood:
3	chr15:41149915..41158340-chr15:41160487..41168241,17	MCF-7	breast:
4	chr15:41148610..41153040-chr15:41153153..41159814,9	MCF-7	breast:
5	chr15:41154418..41156417-chr15:41177527..41179502,2	K562	blood:
6	chr15:41146918..41148656-chr15:41155064..41156700,2	K562	blood:
7	chr15:41149030..41159900-chr15:41180834..41187281,18	MCF-7	breast:
8	chr15:41152386..41154542-chr15:41154856..41158278,3	MCF-7	breast:
9	chr15:41148133..41159834-chr15:41169228..41175193,12	MCF-7	breast:
10	chr15:41137927..41140333-chr15:41154449..41156600,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166145	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1049598	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs11070298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070299	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070304	0.88[EUR][1000 genomes]
rs11856227	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12148523	0.82[EUR][1000 genomes]
rs12903603	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12916961	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16971157	0.88[CEU][hapmap]
rs17649	1.00[CHB][hapmap]
rs1814692	0.97[EUR][1000 genomes]
rs2279578	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2412571	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444382	0.90[EUR][1000 genomes]
rs4244581	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384588	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923885	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923886	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923887	0.90[EUR][1000 genomes]
rs4924509	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601436	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs616606	0.85[EUR][1000 genomes]
rs617377	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs618892	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs618916	0.87[EUR][1000 genomes]
rs625058	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs658752	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs676180	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs690136	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs690507	0.90[EUR][1000 genomes]
rs7172280	0.88[CEU][hapmap]
rs8024861	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs8024961	0.88[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs8042095	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8028660	SPINT1	cis	multi-tissue	Pritchard
rs8028660	C15orf56	cis	cerebellum	SCAN
rs8028660	MGA	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
2	chr15:41149600-41158000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:41149800-41158200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:41150000-41158200	Weak transcription	HMEC	breast
5	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
6	chr15:41150600-41158200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:41151600-41158400	Weak transcription	Fetal Thymus	thymus
8	chr15:41151600-41165400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:41152000-41158000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:41152000-41163800	Weak transcription	Gastric	stomach
11	chr15:41153600-41159200	Enhancers	Stomach Mucosa	stomach
12	chr15:41153800-41156600	Enhancers	Fetal Intestine Large	intestine
13	chr15:41154000-41162400	Weak transcription	GM12878-XiMat	blood
14	chr15:41154400-41156200	Weak transcription	NHEK	skin
15	chr15:41154600-41158000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:41154600-41158000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:41154600-41158400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:41155000-41157000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:41155200-41157200	Enhancers	Duodenum Mucosa	Duodenum
20	chr15:41155200-41157600	Enhancers	Esophagus	oesophagus
21	chr15:41155800-41156200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr15:41155800-41156400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41155800-41156400	Bivalent Enhancer	Fetal Stomach	stomach
24	chr15:41155800-41156600	Enhancers	Fetal Intestine Small	intestine
25	chr15:41155800-41156800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:41155800-41159000	Enhancers	Pancreas	Pancrea
27	chr15:41156000-41156600	Flanking Active TSS	Hela-S3	cervix
28	chr15:41156000-41156600	Enhancers	K562	blood
29	chr15:41156000-41156800	Enhancers	Colonic Mucosa	Colon
30	chr15:41156000-41156800	Flanking Active TSS	HepG2	liver
31	chr15:41156000-41157000	Enhancers	A549	lung
32	chr15:41156000-41159000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links