Variant report

Variant	rs10054158
Chromosome Location	chr5:112386154-112386155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112384421..112386665-chr5:112391243..112394084,2	MCF-7	breast:
2	chr5:112381725..112385379-chr5:112386016..112389315,3	MCF-7	breast:
3	chr5:112384021..112386512-chr5:112388336..112390508,4	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10039618	0.80[CHB][hapmap]
rs10477486	0.85[CHB][hapmap]
rs11749921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2227947	0.85[CHB][hapmap]
rs2227948	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3857434	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs4073358	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073359	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4074190	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075350	0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs4235788	0.84[CHB][hapmap]
rs4301226	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs4428399	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4463174	0.85[CHB][hapmap]
rs4599529	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705750	0.82[GIH][hapmap]
rs4705752	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs4705755	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705756	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705758	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705763	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705767	0.84[ASN][1000 genomes]
rs6594665	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6862481	0.84[CHB][hapmap]
rs6877570	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6877769	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6893016	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893389	0.85[CHB][hapmap]
rs6894219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6894937	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71590730	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7708603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730767	0.85[CHB][hapmap]
rs7731890	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732198	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv516887	chr5:112379659-112396174	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10054158	MCC	cis	Whole Blood	GTEx
rs10054158	TSLP	cis	parietal	SCAN
rs10054158	DCP2	cis	multi-tissue	Pritchard
rs10054158	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs10054158	DCP2	cis	lymphoblastoid	seeQTL
rs10054158	MCC	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
4	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:112374800-112386200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
17	chr5:112377400-112386400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
19	chr5:112379600-112386400	Weak transcription	Brain Angular Gyrus	brain
20	chr5:112379600-112386400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:112379600-112388800	Weak transcription	Gastric	stomach
22	chr5:112379600-112388800	Weak transcription	Spleen	Spleen
23	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
25	chr5:112379800-112386200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:112379800-112386400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:112379800-112388800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:112382600-112386200	Genic enhancers	Fetal Muscle Leg	muscle
29	chr5:112382600-112387200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:112382600-112387400	Enhancers	Placenta	Placenta
31	chr5:112383200-112409400	Strong transcription	Liver	Liver
32	chr5:112383400-112386200	Weak transcription	Osteobl	bone
33	chr5:112383400-112386400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112383400-112386400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:112383400-112395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:112383600-112386200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:112383600-112386200	Weak transcription	HSMM	muscle
38	chr5:112383600-112392000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:112383600-112394200	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:112383800-112386200	Weak transcription	Hela-S3	cervix
41	chr5:112383800-112386200	Weak transcription	NH-A	brain
42	chr5:112383800-112386400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:112383800-112389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:112383800-112393000	Weak transcription	Brain Germinal Matrix	brain
45	chr5:112383800-112394000	Weak transcription	Fetal Thymus	thymus
46	chr5:112384000-112386200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:112384000-112386200	Weak transcription	HUVEC	blood vessel
48	chr5:112384000-112386200	Strong transcription	NHEK	skin
49	chr5:112384000-112386400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:112384000-112386400	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links