Variant report

Variant	rs28625019
Chromosome Location	chr12:123907563-123907564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123899774..123903276-chr12:123906131..123908571,3	K562	blood:
2	chr12:123900528..123903276-chr12:123907055..123908571,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1060105	0.94[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs11830103	0.84[CEU][hapmap]
rs12298826	0.82[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap]
rs12299125	0.80[EUR][1000 genomes]
rs12316131	0.82[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs12322888	0.82[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap]
rs12817892	0.91[CEU][hapmap]
rs1402275	0.87[GIH][hapmap]
rs1716170	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1716171	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1879380	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1969354	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs2337934	0.87[GIH][hapmap];0.91[TSI][hapmap]
rs28372579	0.85[EUR][1000 genomes]
rs28376121	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28406193	0.89[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28410896	0.90[EUR][1000 genomes]
rs28458312	0.82[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs28472704	0.89[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28481863	0.98[EUR][1000 genomes]
rs28569885	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs28576953	0.88[EUR][1000 genomes]
rs28583837	0.80[EUR][1000 genomes]
rs28636834	0.89[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs28676499	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28706696	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715490	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28855757	0.85[EUR][1000 genomes]
rs4759371	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs4759415	0.90[GIH][hapmap];0.91[TSI][hapmap]
rs4930718	0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4930719	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953929	0.87[GIH][hapmap]
rs7980687	0.88[CEU][hapmap]

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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28625019	PITPNM2	cis	cerebellum	SCAN
rs28625019	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28625019	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28625019	CDK2AP1	cis	lymphoblastoid	seeQTL
rs28625019	ANAPC5	cis	parietal	SCAN
rs28625019	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28625019	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28625019	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28625019	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28625019	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 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	chr12:123889600-123917000	Weak transcription	K562	blood
3	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
4	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
5	chr12:123891400-123908600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
8	chr12:123892000-123911400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:123892200-123910000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:123892200-123916800	Weak transcription	NHEK	skin
11	chr12:123892200-123920200	Weak transcription	NH-A	brain
12	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
14	chr12:123893800-123908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:123893800-123909600	Weak transcription	Brain Germinal Matrix	brain
16	chr12:123894000-123907800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
18	chr12:123894200-123908000	Weak transcription	Fetal Intestine Large	intestine
19	chr12:123894200-123911600	Weak transcription	Esophagus	oesophagus
20	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
22	chr12:123894800-123908200	Weak transcription	Fetal Intestine Small	intestine
23	chr12:123894800-123911600	Weak transcription	Colonic Mucosa	Colon
24	chr12:123894800-123920000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:123895200-123911600	Weak transcription	Fetal Lung	lung
26	chr12:123895200-123918200	Weak transcription	Pancreas	Pancrea
27	chr12:123895200-123920000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:123895200-123920000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:123895200-123920000	Weak transcription	HSMM	muscle
30	chr12:123895200-123920000	Weak transcription	NHLF	lung
31	chr12:123895200-123920200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:123895200-123920200	Weak transcription	A549	lung
33	chr12:123895400-123911600	Weak transcription	Brain Substantia Nigra	brain
34	chr12:123896200-123909400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:123896200-123911800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:123896200-123915600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:123896200-123915800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:123896400-123916200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:123896600-123908000	Strong transcription	Lung	lung
40	chr12:123897000-123908000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:123898400-123909600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:123899000-123907600	Strong transcription	Spleen	Spleen
43	chr12:123899400-123907800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:123899400-123908600	Strong transcription	Fetal Stomach	stomach
45	chr12:123899400-123909400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:123899600-123907800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:123899600-123907800	Strong transcription	Liver	Liver
48	chr12:123899600-123908200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:123899600-123908400	Strong transcription	Primary T cells from cord blood	blood
50	chr12:123899600-123916000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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