Variant report

Variant	rs6496994
Chromosome Location	chr15:93383740-93383741
allele	A/T
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	chr15:93373081..93377290-chr15:93381619..93384453,4	K562	blood:
2	chr15:93380005..93386167-chr15:93423963..93429522,11	MCF-7	breast:
3	chr15:93371759..93374581-chr15:93381519..93384451,2	K562	blood:
4	chr15:93383199..93384758-chr15:93447586..93450071,2	MCF-7	breast:
5	chr15:93374832..93376702-chr15:93383011..93385007,2	K562	blood:
6	chr15:93374429..93376523-chr15:93383675..93386464,2	MCF-7	breast:
7	chr15:93352585..93355204-chr15:93381631..93384921,5	MCF-7	breast:
8	chr15:93383122..93385870-chr15:93386846..93388717,2	MCF-7	breast:
9	chr15:93382068..93384905-chr15:93428650..93430651,2	MCF-7	breast:
10	chr15:93380616..93384575-chr15:93388777..93392228,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264173	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000173575	Chromatin interaction
ENSG00000272888	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11074108	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11074109	0.84[AMR][1000 genomes]
rs11074110	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11074111	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12591890	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12592319	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28360722	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28445686	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28613292	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734059	0.84[ASN][1000 genomes]
rs4077882	0.83[CEU][hapmap]
rs4408491	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777740	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4777741	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4777742	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4778045	0.82[AMR][1000 genomes]
rs66967198	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7184028	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023522	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026478	0.83[AMR][1000 genomes]
rs8027176	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8027321	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028071	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8029902	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8030383	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031163	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6496994	MRPS11	cis	parietal	SCAN
rs6496994	C15orf58	cis	cerebellum	SCAN
rs6496994	FAM174B	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93376800-93387000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:93377000-93387200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:93377200-93388000	Weak transcription	Brain Angular Gyrus	brain
4	chr15:93377800-93386600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:93379000-93387000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:93380400-93385000	Enhancers	Fetal Thymus	thymus
7	chr15:93380800-93384600	Enhancers	Thymus	Thymus
8	chr15:93381200-93383800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:93381400-93384000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr15:93381400-93384200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:93381400-93384800	Enhancers	Primary T cells from cord blood	blood
12	chr15:93381400-93385000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr15:93381600-93384200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:93381800-93386800	Weak transcription	HSMMtube	muscle
15	chr15:93382000-93384800	Enhancers	Placenta	Placenta
16	chr15:93382400-93385400	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:93382600-93384000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:93382800-93383800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr15:93382800-93383800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:93382800-93384000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr15:93382800-93384000	Enhancers	NHEK	skin
22	chr15:93383000-93383800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:93383000-93383800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:93383000-93383800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr15:93383000-93383800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:93383000-93383800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr15:93383000-93383800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:93383000-93383800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr15:93383000-93383800	Enhancers	Gastric	stomach
30	chr15:93383000-93383800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr15:93383000-93383800	Enhancers	Spleen	Spleen
32	chr15:93383000-93383800	Enhancers	HMEC	breast
33	chr15:93383000-93383800	Enhancers	HSMM	muscle
34	chr15:93383000-93383800	Enhancers	K562	blood
35	chr15:93383000-93384000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:93383000-93384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:93383000-93384000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr15:93383000-93384000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:93383000-93384000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:93383000-93384000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:93383000-93384000	Enhancers	Pancreas	Pancrea
42	chr15:93383000-93384200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:93383000-93384200	Enhancers	Esophagus	oesophagus
44	chr15:93383200-93383800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:93383200-93383800	Enhancers	Lung	lung
46	chr15:93383200-93384400	Enhancers	Primary B cells from cord blood	blood
47	chr15:93383200-93386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:93383200-93386600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:93383400-93383800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr15:93383400-93383800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links