Variant report

Variant	rs28569885
Chromosome Location	chr12:123897177-123897178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123889002..123891622-chr12:123895728..123898606,2	K562	blood:
2	chr12:123867246..123869776-chr12:123896994..123899843,2	K562	blood:
3	chr12:123871220..123876084-chr12:123892723..123900288,8	K562	blood:
4	chr12:123894977..123897408-chr12:124087588..124090570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111364	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1060105	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs12298826	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs12316131	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs12322888	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs12817892	0.82[CEU][hapmap]
rs1402275	0.87[GIH][hapmap]
rs1716160	0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1716170	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1716171	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1727323	0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1790131	0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1879380	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs1969354	0.84[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs2337934	0.87[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs28372579	0.82[EUR][1000 genomes]
rs28376121	0.90[EUR][1000 genomes]
rs28406193	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28410896	0.88[EUR][1000 genomes]
rs28458312	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs28472704	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28481863	0.95[EUR][1000 genomes]
rs28576953	0.85[EUR][1000 genomes]
rs28625019	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs28636834	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs28676499	0.95[EUR][1000 genomes]
rs28706696	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs28715490	0.96[EUR][1000 genomes]
rs28855757	0.83[EUR][1000 genomes]
rs4759371	0.90[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs4759415	0.90[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs4930718	0.97[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs4930719	0.95[EUR][1000 genomes]
rs7953929	0.87[GIH][hapmap]
rs7980687	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers 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 miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28569885	PITPNM2	cis	cerebellum	SCAN
rs28569885	HIP1R	cis	parietal	SCAN
rs28569885	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28569885	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28569885	ANAPC5	cis	parietal	SCAN
rs28569885	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28569885	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28569885	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28569885	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28569885	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123887000-123897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:123889600-123902600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:123889600-123917000	Weak transcription	K562	blood
5	chr12:123889800-123902800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
7	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
8	chr12:123891400-123908600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
11	chr12:123891800-123900000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:123892000-123899600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:123892000-123899600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:123892000-123903800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:123892000-123911400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:123892200-123901200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:123892200-123905200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:123892200-123905200	Weak transcription	Brain Angular Gyrus	brain
19	chr12:123892200-123905200	Weak transcription	HMEC	breast
20	chr12:123892200-123910000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:123892200-123916800	Weak transcription	NHEK	skin
22	chr12:123892200-123920200	Weak transcription	NH-A	brain
23	chr12:123892400-123899600	Weak transcription	HepG2	liver
24	chr12:123892600-123907000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:123892800-123900000	Weak transcription	Aorta	Aorta
26	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:123893400-123905200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
29	chr12:123893600-123898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:123893600-123905200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:123893600-123905200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:123893800-123905200	Weak transcription	Gastric	stomach
33	chr12:123893800-123908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:123893800-123909600	Weak transcription	Brain Germinal Matrix	brain
35	chr12:123894000-123907800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
37	chr12:123894200-123899600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:123894200-123899600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:123894200-123899800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:123894200-123905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:123894200-123905400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:123894200-123908000	Weak transcription	Fetal Intestine Large	intestine
43	chr12:123894200-123911600	Weak transcription	Esophagus	oesophagus
44	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
46	chr12:123894400-123899600	Weak transcription	Placenta	Placenta
47	chr12:123894400-123905200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:123894400-123905200	Weak transcription	Osteobl	bone
49	chr12:123894400-123907000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:123894800-123899600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links