Variant report

Variant	rs11860484
Chromosome Location	chr16:46946318-46946319
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr16:46946198-46946427	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr16:46946116-46947347	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:46945888-46946486	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:46945940-46946403	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:46945523-46946337	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:46946001-46946398	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:46890264..46892011-chr16:46944513..46947246,2	MCF-7	breast:
2	chr16:46937070..46939899-chr16:46944886..46947118,2	K562	blood:
3	chr16:46936280..46939899-chr16:46944603..46947118,3	K562	blood:

Variant related genes	Relation type
GPT2	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1009391	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10468399	0.82[GIH][hapmap]
rs11861896	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931259	0.82[EUR][1000 genomes]
rs12934580	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.99[EUR][1000 genomes]
rs1641122	1.00[ASN][1000 genomes]
rs1651654	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs166161	0.82[GIH][hapmap]
rs16948661	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs17189741	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs1869006	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	1.00[ASN][1000 genomes]
rs35354454	0.82[EUR][1000 genomes]
rs36471	0.82[GIH][hapmap]
rs36481	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs40355	0.82[GIH][hapmap]
rs4246381	0.92[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401068	0.90[GIH][hapmap]
rs4966706	0.92[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	1.00[GIH][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56042735	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57127559	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	1.00[ASN][1000 genomes]
rs58074838	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59708508	0.87[EUR][1000 genomes]
rs62057633	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	1.00[ASN][1000 genomes]
rs7186748	0.99[EUR][1000 genomes]
rs7187475	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7192574	0.94[EUR][1000 genomes]
rs7196375	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7197485	0.90[GIH][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734309	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs8044443	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs8051017	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8053137	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	1.00[ASN][1000 genomes]
rs8058734	1.00[ASN][1000 genomes]
rs808432	1.00[ASN][1000 genomes]
rs808783	0.90[GIH][hapmap]
rs9328668	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	8 gene(s)	inside rSNPs	diseases
8	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1799095	chr16:46916670-46972671	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1063660	chr16:46930623-46978792	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11860484	SHCBP1	cis	parietal	SCAN
rs11860484	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46919000-46963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:46920800-46949000	Weak transcription	A549	lung
3	chr16:46928400-46966000	Strong transcription	Fetal Brain Female	brain
4	chr16:46929000-46949200	Weak transcription	Fetal Brain Male	brain
5	chr16:46929200-46949200	Weak transcription	K562	blood
6	chr16:46929400-46965200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:46930600-46956200	Weak transcription	Fetal Intestine Small	intestine
8	chr16:46930800-46965400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
10	chr16:46931000-46946800	Weak transcription	Fetal Lung	lung
11	chr16:46931000-46949000	Weak transcription	Fetal Kidney	kidney
12	chr16:46931000-46951200	Strong transcription	Liver	Liver
13	chr16:46931200-46952400	Weak transcription	Ovary	ovary
14	chr16:46931600-46957800	Strong transcription	Fetal Stomach	stomach
15	chr16:46931600-46965200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr16:46932200-46956200	Weak transcription	Left Ventricle	heart
17	chr16:46932200-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr16:46932400-46957600	Weak transcription	Psoas Muscle	Psoas
19	chr16:46933600-46949200	Weak transcription	HSMM	muscle
20	chr16:46933600-46959800	Weak transcription	HUVEC	blood vessel
21	chr16:46933600-46965400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:46933800-46946600	Weak transcription	NH-A	brain
23	chr16:46933800-46965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr16:46934000-46946800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr16:46934000-46963400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:46935400-46958200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr16:46936400-46951800	Weak transcription	Spleen	Spleen
28	chr16:46936600-46956000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr16:46936600-46956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr16:46937800-46949000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr16:46938400-46948600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:46938600-46952600	Weak transcription	Stomach Mucosa	stomach
33	chr16:46938800-46949000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr16:46939600-46964800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:46939800-46949200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr16:46940000-46964600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:46941200-46949400	Weak transcription	Fetal Heart	heart
38	chr16:46941200-46955000	Enhancers	Primary B cells from peripheral blood	blood
39	chr16:46942400-46952000	Strong transcription	HMEC	breast
40	chr16:46942600-46950600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr16:46942800-46947200	Strong transcription	NHEK	skin
42	chr16:46942800-46956200	Weak transcription	Colon Smooth Muscle	Colon
43	chr16:46943000-46952200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:46943000-46952400	Strong transcription	Placenta	Placenta
45	chr16:46943000-46952400	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr16:46943200-46947000	Genic enhancers	Brain Anterior Caudate	brain
47	chr16:46943200-46965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr16:46943200-46965400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr16:46943400-46946400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr16:46943400-46947400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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