Variant report

Variant	rs4072828
Chromosome Location	chr16:81888237-81888238
allele	C/G
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	POLR2A	chr16:81888115-81888263	GM12878	blood:	n/a	n/a
2	RCOR1	chr16:81888208-81888512	K562	blood:	n/a	n/a
3	POLR2A	chr16:81887375-81888461	GM12891	blood:	n/a	n/a
4	ZNF143	chr16:81888190-81888507	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81885841..81888862-chr16:81895847..81897898,3	K562	blood:

Variant related genes	Relation type
PLCG2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1143686	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443578	0.90[AMR][1000 genomes]
rs12446549	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12446576	0.90[AMR][1000 genomes]
rs12446621	0.90[AMR][1000 genomes]
rs12447177	0.89[AMR][1000 genomes]
rs12917936	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12917955	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12922252	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12926118	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12930443	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12930760	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12931199	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12931725	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12932333	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28668056	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34107670	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35386949	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35554443	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4072683	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4072830	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4072831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41309272	0.85[ASN][1000 genomes]
rs4522412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55829397	0.88[ASN][1000 genomes]
rs55856197	0.93[ASN][1000 genomes]
rs56188311	0.88[ASN][1000 genomes]
rs62045706	0.81[ASN][1000 genomes]
rs7184243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186146	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188868	0.86[ASN][1000 genomes]
rs7191743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193477	0.88[ASN][1000 genomes]
rs7500467	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
2	nsv573365	chr16:81804972-81975892	Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1065088	chr16:81878481-81953248	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81866800-81898600	Weak transcription	Right Atrium	heart
2	chr16:81871200-81897200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:81876200-81918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:81876400-81889400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:81877000-81889200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:81877800-81890400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr16:81880000-81889000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr16:81880000-81889200	Weak transcription	Lung	lung
9	chr16:81880000-81911200	Weak transcription	Pancreas	Pancrea
10	chr16:81880400-81908200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr16:81882800-81897200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:81884400-81897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:81886000-81889600	Weak transcription	Right Ventricle	heart
14	chr16:81886200-81894400	Weak transcription	Small Intestine	intestine
15	chr16:81886400-81892800	Strong transcription	GM12878-XiMat	blood
16	chr16:81886400-81896400	Strong transcription	Primary B cells from cord blood	blood
17	chr16:81886600-81888400	Weak transcription	Fetal Intestine Small	intestine
18	chr16:81886600-81889400	Weak transcription	Spleen	Spleen
19	chr16:81886600-81892400	Weak transcription	Placenta	Placenta
20	chr16:81886600-81894600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr16:81887200-81889200	Weak transcription	Adipose Nuclei	Adipose
22	chr16:81887400-81889000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr16:81887400-81894800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr16:81887600-81897000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr16:81887600-81901800	Weak transcription	Fetal Kidney	kidney
26	chr16:81887800-81889400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr16:81887800-81897400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr16:81887800-81899000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr16:81888000-81889400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr16:81888000-81890200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr16:81888000-81894000	Weak transcription	Liver	Liver
32	chr16:81888000-81894200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:81888000-81896800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr16:81888200-81897600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links