Variant report

Variant	rs10848428
Chromosome Location	chr12:123572495-123572496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123570325..123572939-chr12:123584835..123587723,2	K562	blood:
2	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
3	chr12:123572033..123574243-chr12:123627306..123629802,2	MCF-7	breast:
4	chr12:123558779..123562598-chr12:123568640..123572609,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10773002	0.83[ASW][hapmap]
rs10773921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10846489	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs11060853	0.81[JPT][hapmap]
rs1109559	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11608811	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610710	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11613937	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12229700	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12425009	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568427	0.83[ASW][hapmap]
rs1568428	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1611973	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1615350	0.83[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1626703	0.84[AFR][1000 genomes]
rs1716184	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727286	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727293	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1727301	0.85[JPT][hapmap]
rs1727302	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1727305	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727312	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790088	0.82[AMR][1000 genomes]
rs1790094	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790096	0.84[AFR][1000 genomes]
rs1790104	0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1790106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790121	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790122	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790129	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879379	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1984658	0.81[EUR][1000 genomes]
rs2682427	0.85[JPT][hapmap]
rs28755851	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3759115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3897102	1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4148862	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148863	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs4275659	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs585522	0.80[GIH][hapmap]
rs61955214	0.80[ASN][1000 genomes]
rs7135296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7139321	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs7304782	0.83[ASW][hapmap]
rs7305511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884956	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs940904	0.80[GIH][hapmap]
rs949143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10848428	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10848428	TMEM120B	cis	parietal	SCAN
rs10848428	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10848428	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10848428	C12orf65	cis	cerebellum	SCAN
rs10848428	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10848428	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10848428	CDK2AP1	cis	cerebellum	SCAN
rs10848428	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10848428	PITPNM2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123560600-123574200	Weak transcription	Gastric	stomach
2	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
3	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
5	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:123562200-123572600	Weak transcription	K562	blood
7	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
9	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
10	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:123569000-123574000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123569400-123574600	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:123569600-123573800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:123569800-123576200	Weak transcription	Ovary	ovary
17	chr12:123569800-123578200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:123569800-123579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:123570000-123574800	Enhancers	Primary B cells from cord blood	blood
20	chr12:123570000-123579800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:123570600-123572600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:123570600-123573200	Weak transcription	GM12878-XiMat	blood
23	chr12:123570600-123573400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:123570600-123573400	Weak transcription	Psoas Muscle	Psoas
25	chr12:123570600-123573400	Weak transcription	HSMMtube	muscle
26	chr12:123570600-123573400	Weak transcription	NH-A	brain
27	chr12:123570600-123573400	Weak transcription	NHDF-Ad	bronchial
28	chr12:123570600-123573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:123570600-123574000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:123570600-123578600	Weak transcription	Aorta	Aorta
31	chr12:123570600-123578600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:123570600-123578600	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:123570600-123578800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:123570800-123572800	Weak transcription	HSMM	muscle
35	chr12:123570800-123573000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:123570800-123573200	Weak transcription	Liver	Liver
37	chr12:123570800-123573400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:123570800-123573400	Weak transcription	Osteobl	bone
39	chr12:123570800-123573800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:123570800-123573800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:123570800-123574200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:123570800-123574200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:123570800-123578200	Weak transcription	Stomach Mucosa	stomach
44	chr12:123570800-123578600	Weak transcription	Pancreas	Pancrea
45	chr12:123570800-123580200	Enhancers	HMEC	breast
46	chr12:123570800-123586600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:123571000-123572600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:123571000-123573400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:123571000-123573400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:123571000-123575600	Weak transcription	Spleen	Spleen

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