Variant report

Variant	rs804885
Chromosome Location	chr16:81095363-81095364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81093322..81097410-chr16:81102754..81106923,4	MCF-7	breast:
2	chr16:81093718..81096458-chr16:81477922..81479889,2	K562	blood:
3	chr16:81093754..81095861-chr16:81110102..81112383,2	MCF-7	breast:
4	chr16:81094141..81096818-chr16:81110183..81111758,2	K562	blood:

Variant related genes	Relation type
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000153815	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1035541	0.81[EUR][1000 genomes]
rs10459871	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[EUR][1000 genomes]
rs10459872	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[EUR][1000 genomes]
rs1048194	0.89[CEU][hapmap]
rs10514512	1.00[CEU][hapmap]
rs10514513	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs10514514	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs10514515	1.00[CEU][hapmap]
rs11150337	0.96[EUR][1000 genomes]
rs11537	1.00[CEU][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes]
rs11863158	0.95[EUR][1000 genomes]
rs11865207	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11866124	0.90[CEU][hapmap]
rs12443549	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs12444137	1.00[CEU][hapmap]
rs12444747	0.89[CEU][hapmap]
rs12444969	0.85[EUR][1000 genomes]
rs12444974	0.90[CEU][hapmap]
rs12445303	1.00[CEU][hapmap]
rs12456	0.89[CEU][hapmap]
rs12927239	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12927828	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13185	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1414	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs1563072	0.90[CEU][hapmap]
rs1563075	1.00[CEU][hapmap]
rs16954505	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs16954513	0.89[CEU][hapmap]
rs16954572	1.00[CEU][hapmap]
rs16954582	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs2257378	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2278022	0.89[CEU][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs2278024	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2278025	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2287995	0.88[EUR][1000 genomes]
rs2316730	0.89[CEU][hapmap]
rs2316731	0.86[CEU][hapmap]
rs2549891	1.00[CEU][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2549892	0.86[ASN][1000 genomes]
rs2549895	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549896	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2549899	0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602401	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs2602402	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602404	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602431	0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[MKK][hapmap];0.85[ASN][1000 genomes]
rs2873310	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2911159	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2970076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2970077	0.89[CEU][hapmap];0.80[LWK][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs35096487	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4324141	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs4454990	0.89[CEU][hapmap];0.93[MEX][hapmap]
rs4889225	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4889229	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889230	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889233	0.90[CEU][hapmap]
rs58144189	0.85[EUR][1000 genomes]
rs6420421	0.90[CEU][hapmap]
rs7185637	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7203546	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7204040	1.00[CEU][hapmap]
rs7206814	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754429	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8043855	1.00[CEU][hapmap]
rs804895	0.88[ASW][hapmap];0.90[CEU][hapmap];0.84[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs804896	0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs804897	0.81[EUR][1000 genomes]
rs804902	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs804903	0.88[ASN][1000 genomes]
rs804904	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs804905	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8052415	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8052490	1.00[CEU][hapmap]
rs8056972	1.00[CEU][hapmap]
rs8059692	0.90[CEU][hapmap]
rs8177940	1.00[CEU][hapmap]
rs8177957	1.00[CEU][hapmap]
rs8177959	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs889516	0.84[EUR][1000 genomes]
rs935942	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806918	0.85[EUR][1000 genomes]
rs9923732	1.00[CEU][hapmap]
rs9925940	1.00[CEU][hapmap]
rs9925943	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs9926174	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs9929586	1.00[CEU][hapmap]
rs9933184	1.00[CEU][hapmap];0.87[MEX][hapmap]

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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	71 gene(s)	inside rSNPs	diseases
5	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs804885	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs804885	ATMIN	cis	Muscle Skeletal	GTEx
rs804885	LOC100329108	cis	lymphoblastoid	seeQTL
rs804885	C16orf61	cis	cerebellum	SCAN
rs804885	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs804885	CENPN	cis	parietal	SCAN
rs804885	GCSH	cis	Muscle Skeletal	GTEx
rs804885	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs804885	C16orf46	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81079400-81109800	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:81080400-81110200	Weak transcription	Ovary	ovary
3	chr16:81083800-81099800	Weak transcription	Brain Angular Gyrus	brain
4	chr16:81088800-81095400	Weak transcription	Fetal Stomach	stomach
5	chr16:81090200-81097600	Weak transcription	Pancreas	Pancrea
6	chr16:81092000-81106600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:81093000-81109800	Weak transcription	Brain Anterior Caudate	brain
8	chr16:81093200-81100200	Weak transcription	Brain Germinal Matrix	brain
9	chr16:81093600-81100000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:81094200-81095600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:81094200-81095600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:81094200-81096000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:81094400-81095400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr16:81094400-81095400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr16:81094400-81095600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr16:81094400-81095600	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr16:81094400-81096200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr16:81094600-81098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:81094800-81095600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr16:81094800-81095600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr16:81095000-81095400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:81095000-81095600	Enhancers	Fetal Muscle Trunk	muscle
23	chr16:81095000-81109400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links