Variant report

Variant	rs4889442
Chromosome Location	chr16:81961873-81961874
allele	G/T
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	chr16:81957443-81962184	GM12892	blood:	n/a	n/a
2	POLR2A	chr16:81960441-81962131	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81959648..81962343-chr16:82020413..82022447,2	K562	blood:
2	chr16:81958643..81960384-chr16:81960629..81962269,2	K562	blood:
3	chr16:81959537..81963642-chr16:81965973..81970581,4	K562	blood:
4	chr16:81947720..81949312-chr16:81961811..81964487,2	MCF-7	breast:

Variant related genes	Relation type
PLCG2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12445489	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12446596	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12448089	0.87[EUR][1000 genomes]
rs12716924	0.89[CEU][hapmap];0.96[YRI][hapmap]
rs12716925	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12716926	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12716927	0.89[EUR][1000 genomes]
rs17202296	0.90[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs3813010	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4243224	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4366702	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4888189	0.89[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888190	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564938	0.88[CEU][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7201045	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs8063604	0.83[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8063728	0.94[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9931137	0.89[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4889442	MPHOSPH6	cis	cerebellum	SCAN
rs4889442	CDH13	cis	cerebellum	SCAN
rs4889442	ATMIN	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81920400-81982000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr16:81924400-81970000	Weak transcription	Fetal Intestine Large	intestine
3	chr16:81925800-81992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:81933000-81983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:81934800-81971600	Weak transcription	Right Atrium	heart
6	chr16:81936000-81982000	Weak transcription	Gastric	stomach
7	chr16:81936000-81984600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr16:81937000-81969800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:81941600-81966000	Weak transcription	Placenta	Placenta
10	chr16:81945000-81984600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr16:81946200-81985200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr16:81947000-81969200	Weak transcription	Pancreas	Pancrea
13	chr16:81950600-81982000	Strong transcription	GM12878-XiMat	blood
14	chr16:81951200-81962200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:81951400-81971400	Weak transcription	Left Ventricle	heart
16	chr16:81952000-81982800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr16:81952400-81983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr16:81952600-81970600	Strong transcription	Spleen	Spleen
19	chr16:81952600-81981800	Strong transcription	Primary B cells from cord blood	blood
20	chr16:81952800-81973000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr16:81952800-81984600	Strong transcription	Liver	Liver
22	chr16:81953000-81977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr16:81953400-81962200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:81954800-81962200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr16:81954800-81991800	Weak transcription	Fetal Thymus	thymus
26	chr16:81955400-81970200	Weak transcription	Brain Substantia Nigra	brain
27	chr16:81956400-81971400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:81956400-81971600	Weak transcription	Fetal Kidney	kidney
29	chr16:81956800-81962000	Weak transcription	HMEC	breast
30	chr16:81957000-81971200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:81958200-81962800	Strong transcription	Fetal Intestine Small	intestine
32	chr16:81959600-81983800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:81960000-81966000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr16:81960000-81969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr16:81960200-81962200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr16:81960200-81966600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr16:81960400-81962600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr16:81960600-81965600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr16:81960600-81982400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:81960800-81962200	Weak transcription	Fetal Stomach	stomach
41	chr16:81960800-81963800	Strong transcription	Adipose Nuclei	Adipose
42	chr16:81961200-81963600	Strong transcription	Colonic Mucosa	Colon
43	chr16:81961200-81963800	Strong transcription	Lung	lung
44	chr16:81961600-81963000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:81961600-81963600	Enhancers	Esophagus	oesophagus
46	chr16:81961600-81984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr16:81961800-81963600	Genic enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links