Variant report

Variant	rs1790121
Chromosome Location	chr12:123604492-123604493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123603146..123605205-chr12:123632203..123634341,2	MCF-7	breast:
2	chr12:123604029..123607309-chr12:123609256..123611485,3	K562	blood:
3	chr12:123594098..123598804-chr12:123600213..123604964,5	K562	blood:
4	chr12:123578789..123580705-chr12:123603814..123606258,2	K562	blood:
5	chr12:123598890..123601650-chr12:123601866..123605162,4	K562	blood:
6	chr12:123603321..123605934-chr12:123608527..123611657,3	K562	blood:
7	chr12:123602721..123605164-chr12:123609329..123611695,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

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];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10773003	0.80[JPT][hapmap]
rs10773005	0.80[JPT][hapmap]
rs10773921	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846489	0.90[ASW][hapmap];0.84[CEU][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10848428	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]
rs11057219	0.82[AFR][1000 genomes]
rs11057251	1.00[ASW][hapmap];0.80[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs11060853	0.81[JPT][hapmap]
rs1109559	0.90[ASW][hapmap];0.80[CEU][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11608305	0.80[JPT][hapmap]
rs11608811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11610710	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11613128	0.87[AFR][1000 genomes]
rs11613937	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12229700	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12317452	0.80[JPT][hapmap]
rs12425009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1568428	0.90[ASW][hapmap];0.84[CEU][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1611973	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1615350	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1616484	0.85[AFR][1000 genomes]
rs1626703	0.84[AFR][1000 genomes]
rs1716178	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1716184	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727286	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727293	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[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	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727312	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790088	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790094	1.00[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];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790096	0.84[AFR][1000 genomes]
rs1790104	0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1790106	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790122	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790129	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1790134	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879379	0.90[ASW][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1984658	0.81[EUR][1000 genomes]
rs2337630	0.82[AFR][1000 genomes]
rs2337631	0.82[AFR][1000 genomes]
rs2682427	0.85[JPT][hapmap]
rs28755851	0.80[EUR][1000 genomes]
rs3088303	0.80[JPT][hapmap]
rs34841857	0.82[AFR][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3759115	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3897102	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4148862	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148863	1.00[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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275659	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs4553407	0.82[AFR][1000 genomes]
rs4759377	0.80[JPT][hapmap]
rs585522	0.80[GIH][hapmap]
rs7135296	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7139321	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs7305511	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884956	0.90[ASW][hapmap];0.95[CHB][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs940904	0.80[GIH][hapmap]
rs949143	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1790121	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790121	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790121	ANAPC5	cis	parietal	SCAN
rs1790121	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790121	TMEM120B	cis	parietal	SCAN
rs1790121	PITPNM2	cis	cerebellum	SCAN
rs1790121	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1790121	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790121	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123592800-123611200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:123594600-123607200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:123595200-123610800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:123596600-123604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123597400-123608200	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:123597800-123610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:123598000-123608400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:123598200-123604800	Enhancers	Primary T cells from cord blood	blood
10	chr12:123598600-123606400	Weak transcription	HepG2	liver
11	chr12:123598800-123605000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
13	chr12:123600000-123604800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr12:123600000-123605000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:123600000-123605200	Weak transcription	Fetal Intestine Large	intestine
16	chr12:123600000-123611200	Weak transcription	Aorta	Aorta
17	chr12:123600200-123605200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:123600600-123610600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:123600600-123610800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:123600600-123610800	Weak transcription	Fetal Intestine Small	intestine
21	chr12:123600600-123610800	Weak transcription	Stomach Mucosa	stomach
22	chr12:123600600-123611000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:123600600-123611000	Weak transcription	Small Intestine	intestine
24	chr12:123600800-123604600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:123600800-123604800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:123600800-123604800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:123600800-123605000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr12:123600800-123605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:123600800-123605000	Weak transcription	Hela-S3	cervix
30	chr12:123600800-123605200	Weak transcription	NHEK	skin
31	chr12:123600800-123605400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:123601000-123604800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:123601000-123604800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:123601000-123605200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:123601000-123610600	Weak transcription	Osteobl	bone
36	chr12:123601200-123605000	Weak transcription	HSMM	muscle
37	chr12:123601200-123605400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:123601400-123604800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:123601400-123605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:123601400-123605200	Weak transcription	HSMMtube	muscle
41	chr12:123601400-123611000	Weak transcription	Psoas Muscle	Psoas
42	chr12:123601600-123605000	Weak transcription	Colonic Mucosa	Colon
43	chr12:123601600-123605000	Weak transcription	Esophagus	oesophagus
44	chr12:123601600-123607400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:123601600-123615800	Weak transcription	Pancreas	Pancrea
46	chr12:123601800-123605000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:123602000-123604800	Weak transcription	Brain Anterior Caudate	brain
48	chr12:123602000-123605000	Weak transcription	Liver	Liver
49	chr12:123602000-123605000	Weak transcription	Brain Angular Gyrus	brain
50	chr12:123602000-123605200	Weak transcription	Right Atrium	heart

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