Variant report

Variant	rs1790090
Chromosome Location	chr12:123633424-123633425
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	chr12:123625936..123634145-chr12:123634916..123640513,10	K562	blood:
2	chr12:123624513..123626615-chr12:123631268..123633682,3	K562	blood:
3	chr12:123632948..123634613-chr12:123717747..123719847,2	K562	blood:
4	chr12:123633130..123634910-chr12:123716201..123717715,2	K562	blood:
5	chr12:123633368..123635688-chr12:123701614..123704544,2	MCF-7	breast:
6	chr12:123616297..123618408-chr12:123632574..123634282,2	MCF-7	breast:
7	chr12:123603146..123605205-chr12:123632203..123634341,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1047158	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744147	0.94[EUR][1000 genomes]
rs10772993	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.93[EUR][1000 genomes]
rs10772996	0.80[EUR][1000 genomes]
rs10772998	0.84[EUR][1000 genomes]
rs10846478	0.93[EUR][1000 genomes]
rs10846486	0.90[EUR][1000 genomes]
rs10846487	0.81[EUR][1000 genomes]
rs11057189	0.80[EUR][1000 genomes]
rs11057192	0.93[EUR][1000 genomes]
rs11057204	0.83[EUR][1000 genomes]
rs11057206	0.84[EUR][1000 genomes]
rs11057210	0.83[EUR][1000 genomes]
rs1106240	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106241	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260294	0.86[EUR][1000 genomes]
rs12817892	0.82[EUR][1000 genomes]
rs12818067	0.82[EUR][1000 genomes]
rs12829456	0.82[EUR][1000 genomes]
rs1402274	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1569068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615350	0.83[EUR][1000 genomes]
rs1615694	0.92[EUR][1000 genomes]
rs1616131	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.91[EUR][1000 genomes]
rs1617434	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618679	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.91[EUR][1000 genomes]
rs1627724	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.92[EUR][1000 genomes]
rs1630905	0.93[EUR][1000 genomes]
rs1716156	0.89[EUR][1000 genomes]
rs1716157	0.93[EUR][1000 genomes]
rs1716158	0.86[EUR][1000 genomes]
rs1716159	0.93[EUR][1000 genomes]
rs1716160	0.93[EUR][1000 genomes]
rs1716164	0.91[EUR][1000 genomes]
rs1716165	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	0.85[EUR][1000 genomes]
rs1716171	0.85[EUR][1000 genomes]
rs1716172	0.87[EUR][1000 genomes]
rs1716173	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716175	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716176	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716177	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716182	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1716185	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727290	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727294	0.99[EUR][1000 genomes]
rs1727296	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.91[EUR][1000 genomes]
rs1727302	0.84[EUR][1000 genomes]
rs1727306	0.93[EUR][1000 genomes]
rs1727309	0.91[EUR][1000 genomes]
rs1727310	0.91[EUR][1000 genomes]
rs1727313	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727317	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727320	0.93[EUR][1000 genomes]
rs1727322	0.87[EUR][1000 genomes]
rs1727323	0.93[EUR][1000 genomes]
rs1727324	0.91[EUR][1000 genomes]
rs1727325	0.93[EUR][1000 genomes]
rs1727334	0.85[EUR][1000 genomes]
rs1790086	0.93[EUR][1000 genomes]
rs1790087	0.93[EUR][1000 genomes]
rs1790089	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1790095	0.95[EUR][1000 genomes]
rs1790098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790100	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1790101	0.92[EUR][1000 genomes]
rs1790102	0.92[EUR][1000 genomes]
rs1790108	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790119	0.83[EUR][1000 genomes]
rs1790120	0.89[EUR][1000 genomes]
rs1790123	0.91[EUR][1000 genomes]
rs1790124	0.90[EUR][1000 genomes]
rs1790125	0.85[EUR][1000 genomes]
rs1790130	0.91[EUR][1000 genomes]
rs1790131	0.93[EUR][1000 genomes]
rs2049114	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2510885	0.96[EUR][1000 genomes]
rs2682425	0.85[EUR][1000 genomes]
rs2682429	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.91[EUR][1000 genomes]
rs2682431	0.93[EUR][1000 genomes]
rs2682433	0.91[EUR][1000 genomes]
rs2682434	0.93[EUR][1000 genomes]
rs2695476	0.91[EUR][1000 genomes]
rs2695478	0.93[EUR][1000 genomes]
rs2695479	0.91[EUR][1000 genomes]
rs2695480	0.90[EUR][1000 genomes]
rs2695481	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.89[EUR][1000 genomes]
rs2851436	0.91[EUR][1000 genomes]
rs2851438	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851450	0.93[EUR][1000 genomes]
rs2851451	0.93[EUR][1000 genomes]
rs2947099	0.91[EUR][1000 genomes]
rs2950537	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3018098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34341465	0.82[EUR][1000 genomes]
rs4372492	0.93[EUR][1000 genomes]
rs4460848	0.80[EUR][1000 genomes]
rs4759409	0.82[EUR][1000 genomes]
rs58809476	0.82[EUR][1000 genomes]
rs7299943	0.80[EUR][1000 genomes]
rs7313483	0.81[EUR][1000 genomes]
rs884548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941305	0.85[EUR][1000 genomes]
rs941306	0.85[EUR][1000 genomes]
rs949142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795522	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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 target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790090	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790090	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1790090	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790090	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1790090	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790090	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790090	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123618000-123634200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123625000-123633600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:123625400-123633800	Weak transcription	Fetal Brain Male	brain
5	chr12:123625400-123634600	Weak transcription	Aorta	Aorta
6	chr12:123627000-123634200	Weak transcription	NHEK	skin
7	chr12:123627000-123634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123627200-123634000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:123627200-123634000	Weak transcription	HMEC	breast
10	chr12:123627200-123634000	Weak transcription	HSMMtube	muscle
11	chr12:123627800-123633600	Weak transcription	Stomach Mucosa	stomach
12	chr12:123627800-123633800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:123627800-123634000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123627800-123634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123628000-123633600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:123628000-123633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:123628000-123633600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:123628000-123634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:123628200-123633600	Weak transcription	Fetal Intestine Small	intestine
20	chr12:123628200-123633800	Weak transcription	Fetal Stomach	stomach
21	chr12:123628400-123633600	Weak transcription	Psoas Muscle	Psoas
22	chr12:123628400-123633800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:123628400-123634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:123628600-123633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:123628600-123633600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:123628600-123633800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:123628600-123634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:123628800-123633800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:123628800-123633800	Weak transcription	NHLF	lung
30	chr12:123628800-123634400	Weak transcription	Esophagus	oesophagus
31	chr12:123629000-123633600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:123629000-123633600	Weak transcription	NHDF-Ad	bronchial
33	chr12:123629000-123633800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123629000-123633800	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:123629000-123633800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:123629000-123633800	Weak transcription	NH-A	brain
37	chr12:123629000-123634200	Weak transcription	Osteobl	bone
38	chr12:123630400-123633600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:123630400-123633800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:123630400-123633800	Weak transcription	A549	lung
41	chr12:123630600-123633600	Weak transcription	Hela-S3	cervix
42	chr12:123630600-123633800	Weak transcription	Fetal Kidney	kidney
43	chr12:123631200-123634400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
44	chr12:123631200-123634800	Transcr. at gene 5' and 3'	Thymus	Thymus
45	chr12:123631400-123633800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:123631600-123633800	Enhancers	K562	blood
47	chr12:123631600-123634000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr12:123631600-123634200	Enhancers	Liver	Liver
49	chr12:123631600-123634400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:123631800-123634000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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