Variant report

Variant	rs1790123
Chromosome Location	chr12:123659542-123659543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 164 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1047158	0.91[EUR][1000 genomes]
rs1051431	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1060105	0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs10732573	0.80[CEU][hapmap]
rs10744147	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10772993	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10772995	0.98[EUR][1000 genomes]
rs10772996	0.81[EUR][1000 genomes]
rs10772998	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs10846478	0.98[EUR][1000 genomes]
rs10846486	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10846487	0.82[EUR][1000 genomes]
rs11057189	0.81[EUR][1000 genomes]
rs11057192	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs11057204	0.84[EUR][1000 genomes]
rs11057206	0.84[EUR][1000 genomes]
rs11057210	0.83[EUR][1000 genomes]
rs1106240	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1106241	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs11830103	0.84[CEU][hapmap]
rs12298826	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs12304248	0.89[CEU][hapmap]
rs12316131	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs12322888	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs1260294	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1270594	0.82[AMR][1000 genomes]
rs12817892	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12818067	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12829456	0.86[EUR][1000 genomes]
rs1402274	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1402275	0.90[GIH][hapmap]
rs1463877	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1533703	0.94[CEU][hapmap]
rs1569068	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1609520	0.80[CEU][hapmap]
rs1615350	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1615694	0.97[EUR][1000 genomes]
rs1616131	0.89[EUR][1000 genomes]
rs1616181	0.89[EUR][1000 genomes]
rs1617156	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1617434	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1618679	0.89[EUR][1000 genomes]
rs1621194	0.92[EUR][1000 genomes]
rs1626899	0.92[EUR][1000 genomes]
rs1627724	0.91[EUR][1000 genomes]
rs1630693	0.93[EUR][1000 genomes]
rs1630905	0.93[EUR][1000 genomes]
rs1716156	0.94[EUR][1000 genomes]
rs1716157	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1716158	0.91[EUR][1000 genomes]
rs1716159	0.98[EUR][1000 genomes]
rs1716160	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1716164	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1716165	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1716167	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1716168	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1716170	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1716171	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1716172	0.87[EUR][1000 genomes]
rs1716173	0.94[EUR][1000 genomes]
rs1716174	0.83[EUR][1000 genomes]
rs1716175	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1716176	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1716177	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1716182	0.92[EUR][1000 genomes]
rs1716185	0.88[EUR][1000 genomes]
rs1727290	0.95[EUR][1000 genomes]
rs1727294	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1727296	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1727300	0.96[EUR][1000 genomes]
rs1727302	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1727306	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1727309	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1727310	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1727311	0.82[EUR][1000 genomes]
rs1727313	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1727314	0.89[EUR][1000 genomes]
rs1727315	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1727316	0.89[EUR][1000 genomes]
rs1727317	0.90[EUR][1000 genomes]
rs1727318	0.85[EUR][1000 genomes]
rs1727320	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1727322	0.91[EUR][1000 genomes]
rs1727323	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1727324	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1727325	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1727331	0.80[CEU][hapmap]
rs1727334	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs1790086	0.98[EUR][1000 genomes]
rs1790087	0.98[EUR][1000 genomes]
rs1790089	0.96[EUR][1000 genomes]
rs1790090	0.91[EUR][1000 genomes]
rs1790095	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1790098	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs1790100	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1790101	0.93[EUR][1000 genomes]
rs1790102	0.93[EUR][1000 genomes]
rs1790108	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1790109	0.91[EUR][1000 genomes]
rs1790116	0.94[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1790120	0.83[EUR][1000 genomes]
rs1790124	0.95[EUR][1000 genomes]
rs1790125	0.90[EUR][1000 genomes]
rs1790130	0.92[EUR][1000 genomes]
rs1790131	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1879380	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.94[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.94[CEU][hapmap]
rs2049114	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2102949	0.81[EUR][1000 genomes]
rs2337934	0.94[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]
rs2510885	0.87[EUR][1000 genomes]
rs2682425	0.84[EUR][1000 genomes]
rs2682429	0.91[EUR][1000 genomes]
rs2682430	0.92[EUR][1000 genomes]
rs2682431	0.94[EUR][1000 genomes]
rs2682433	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682434	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2695476	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2695478	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2695479	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2695480	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2695481	0.91[EUR][1000 genomes]
rs2695482	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2851435	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851436	0.96[EUR][1000 genomes]
rs2851438	0.91[EUR][1000 genomes]
rs2851441	0.85[EUR][1000 genomes]
rs2851447	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2851450	0.94[EUR][1000 genomes]
rs2851451	0.93[EUR][1000 genomes]
rs2947099	0.92[EUR][1000 genomes]
rs2950537	0.91[EUR][1000 genomes]
rs3018098	0.95[EUR][1000 genomes]
rs34341465	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4372492	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4460848	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4759371	0.94[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs4759415	0.94[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs520088	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs585522	0.86[TSI][hapmap]
rs58809476	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs641760	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs655293	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7132277	0.89[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs7299943	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7304782	0.80[CEU][hapmap]
rs7313483	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs7953929	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs7980687	0.89[CEU][hapmap]
rs883263	0.88[CEU][hapmap];0.94[TSI][hapmap]
rs884548	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs937564	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs941305	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs941306	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs949142	0.91[EUR][1000 genomes]
rs9795522	0.84[EUR][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	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
2	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
3	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
4	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
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1790123	OGFOD2	cis	lymphoblastoid	seeQTL
rs1790123	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1790123	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790123	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790123	CDK2AP1	cis	lymphoblastoid	seeQTL
rs1790123	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1790123	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790123	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790123	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1790123	PITPNM2	cis	cerebellum	SCAN
rs1790123	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1790123	ANAPC5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:123636600-123676200	Weak transcription	Gastric	stomach
3	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
4	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
5	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
6	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
7	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
12	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:123645400-123660000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:123645600-123660800	Weak transcription	Fetal Brain Male	brain
15	chr12:123647400-123660800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
17	chr12:123648800-123673600	Weak transcription	HMEC	breast
18	chr12:123649200-123660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:123650000-123660600	Weak transcription	Fetal Kidney	kidney
20	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:123650600-123660800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:123650600-123660800	Weak transcription	HSMM	muscle
23	chr12:123650600-123664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:123650600-123664600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:123650600-123671600	Weak transcription	Brain Germinal Matrix	brain
26	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
28	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
29	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:123650800-123663600	Weak transcription	Lung	lung
31	chr12:123651200-123660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:123651200-123661200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:123651200-123670000	Weak transcription	Spleen	Spleen
34	chr12:123651200-123673600	Weak transcription	Brain Substantia Nigra	brain
35	chr12:123651400-123660800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:123651400-123660800	Weak transcription	Osteobl	bone
37	chr12:123651400-123662600	Weak transcription	Brain Anterior Caudate	brain
38	chr12:123651400-123663200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:123651400-123672000	Weak transcription	NHDF-Ad	bronchial
40	chr12:123651400-123673600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:123651400-123673600	Weak transcription	NHEK	skin
42	chr12:123651400-123675800	Weak transcription	Ovary	ovary
43	chr12:123651600-123663600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:123651600-123676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:123652000-123673000	Weak transcription	Aorta	Aorta
46	chr12:123652200-123660600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:123652200-123676200	Weak transcription	Right Ventricle	heart
48	chr12:123652400-123661000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:123652400-123661600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:123652400-123665600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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