Variant report

Variant	rs2695478
Chromosome Location	chr12:123689521-123689522
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	chr12:123681413..123683609-chr12:123687965..123690552,2	K562	blood:

Extended variants
information (count: 167 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1047158	0.93[EUR][1000 genomes]
rs1051431	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1060105	0.86[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs10732573	0.80[CEU][hapmap]
rs10744147	0.91[EUR][1000 genomes]
rs10744148	0.82[EUR][1000 genomes]
rs10772993	0.95[EUR][1000 genomes]
rs10772995	0.96[EUR][1000 genomes]
rs10772996	0.83[EUR][1000 genomes]
rs10772998	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs10846478	0.96[EUR][1000 genomes]
rs10846486	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10846487	0.84[EUR][1000 genomes]
rs11057189	0.83[EUR][1000 genomes]
rs11057192	0.94[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11057204	0.86[EUR][1000 genomes]
rs11057206	0.87[EUR][1000 genomes]
rs11057210	0.85[EUR][1000 genomes]
rs1106240	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1106241	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.92[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	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1270594	0.81[EUR][1000 genomes]
rs12817892	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12818067	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12829456	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1402274	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1402275	0.90[GIH][hapmap]
rs1533703	0.94[CEU][hapmap]
rs1569068	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1609520	0.80[CEU][hapmap]
rs1615350	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1615694	0.95[EUR][1000 genomes]
rs1616131	0.91[EUR][1000 genomes]
rs1616181	0.91[EUR][1000 genomes]
rs1617156	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1617434	0.96[EUR][1000 genomes]
rs1618679	0.91[EUR][1000 genomes]
rs1621194	0.94[EUR][1000 genomes]
rs1626899	0.94[EUR][1000 genomes]
rs1627724	0.93[EUR][1000 genomes]
rs1630693	0.95[EUR][1000 genomes]
rs1630905	0.96[EUR][1000 genomes]
rs1716156	0.91[EUR][1000 genomes]
rs1716157	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1716158	0.89[EUR][1000 genomes]
rs1716159	0.96[EUR][1000 genomes]
rs1716160	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1716164	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1716165	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1716167	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1716168	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1716170	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1716171	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1716172	0.89[EUR][1000 genomes]
rs1716173	0.92[EUR][1000 genomes]
rs1716174	0.81[EUR][1000 genomes]
rs1716175	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1716176	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1716177	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1716182	0.94[EUR][1000 genomes]
rs1716185	0.90[EUR][1000 genomes]
rs1727290	0.97[EUR][1000 genomes]
rs1727294	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1727296	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1727300	0.93[EUR][1000 genomes]
rs1727302	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1727306	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1727309	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1727310	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1727313	1.00[CEU][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727314	0.91[EUR][1000 genomes]
rs1727315	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1727316	0.91[EUR][1000 genomes]
rs1727317	0.93[EUR][1000 genomes]
rs1727318	0.87[EUR][1000 genomes]
rs1727319	0.81[EUR][1000 genomes]
rs1727320	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1727322	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727323	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1727324	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1727325	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1727331	0.80[CEU][hapmap]
rs1727334	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs1790086	0.96[EUR][1000 genomes]
rs1790087	0.96[EUR][1000 genomes]
rs1790089	0.98[EUR][1000 genomes]
rs1790090	0.93[EUR][1000 genomes]
rs1790095	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1790098	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1790100	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1790101	0.95[EUR][1000 genomes]
rs1790102	0.95[EUR][1000 genomes]
rs1790108	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1790109	0.93[EUR][1000 genomes]
rs1790116	0.94[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1790120	0.85[EUR][1000 genomes]
rs1790123	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]
rs1790124	0.93[EUR][1000 genomes]
rs1790125	0.87[EUR][1000 genomes]
rs1790130	0.94[EUR][1000 genomes]
rs1790131	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs1879380	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1969354	0.94[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.94[CEU][hapmap]
rs2049114	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2102949	0.83[EUR][1000 genomes]
rs2337934	0.94[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]
rs2510885	0.89[EUR][1000 genomes]
rs2682425	0.86[EUR][1000 genomes]
rs2682429	0.93[EUR][1000 genomes]
rs2682430	0.94[EUR][1000 genomes]
rs2682431	0.96[EUR][1000 genomes]
rs2682433	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2682434	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2695476	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695479	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2695480	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2695481	0.93[EUR][1000 genomes]
rs2695482	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs28458312	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs28472704	0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs2851435	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2851436	0.93[EUR][1000 genomes]
rs2851438	0.93[EUR][1000 genomes]
rs2851441	0.87[EUR][1000 genomes]
rs2851443	0.82[EUR][1000 genomes]
rs2851447	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2851450	0.96[EUR][1000 genomes]
rs2851451	0.96[EUR][1000 genomes]
rs28636834	0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs2947099	0.94[EUR][1000 genomes]
rs2950537	0.93[EUR][1000 genomes]
rs3018098	0.97[EUR][1000 genomes]
rs34341465	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4372492	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4460848	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4759371	0.94[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.94[CEU][hapmap];0.85[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	0.88[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]
rs6633	0.84[AFR][1000 genomes]
rs7132277	0.84[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[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];0.84[EUR][1000 genomes]
rs7953929	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs7980687	0.89[CEU][hapmap]
rs884548	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs941305	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs941306	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs949142	0.93[EUR][1000 genomes]
rs9795522	0.87[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
rs2695478	MPHOSPH9	cis	multi-tissue	Pritchard
rs2695478	ANAPC5	cis	parietal	SCAN
rs2695478	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs2695478	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs2695478	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2695478	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs2695478	CDK2AP1	cis	multi-tissue	Pritchard
rs2695478	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs2695478	OGFOD2	cis	brain	seeQTL
rs2695478	CDK2AP1	cis	lymphoblastoid	seeQTL
rs2695478	OGFOD2	trans	brain	seeQTL
rs2695478	PITPNM2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
2	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123665800-123703800	Weak transcription	Stomach Mucosa	stomach
13	chr12:123667600-123695000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:123668200-123703600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:123669200-123695400	Strong transcription	Dnd41	blood
16	chr12:123669600-123701200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:123674000-123693200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:123674000-123706000	Weak transcription	HMEC	breast
19	chr12:123674600-123713400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:123676400-123696600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:123677000-123694000	Weak transcription	Lung	lung
22	chr12:123678800-123698200	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:123678800-123706600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:123680600-123716600	Weak transcription	Colonic Mucosa	Colon
25	chr12:123680800-123695200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:123683600-123695400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123684000-123707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:123684000-123709800	Strong transcription	Liver	Liver
29	chr12:123684200-123694600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:123684400-123690800	Strong transcription	K562	blood
31	chr12:123684400-123695000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:123684600-123692000	Strong transcription	GM12878-XiMat	blood
33	chr12:123684800-123695200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:123685000-123708400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:123685200-123690800	Strong transcription	Fetal Lung	lung
36	chr12:123685200-123697600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:123685200-123700000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:123685400-123692000	Strong transcription	Primary B cells from cord blood	blood
39	chr12:123685400-123694200	Strong transcription	Fetal Brain Female	brain
40	chr12:123685400-123698000	Strong transcription	Fetal Thymus	thymus
41	chr12:123685400-123711600	Strong transcription	Fetal Stomach	stomach
42	chr12:123685600-123694200	Strong transcription	Placenta	Placenta
43	chr12:123685600-123694600	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:123685600-123696800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:123685800-123694200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:123685800-123695400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:123685800-123701200	Strong transcription	Primary T cells from cord blood	blood
48	chr12:123685800-123701600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:123685800-123701600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:123685800-123704600	Strong transcription	Primary T cells fromperipheralblood	blood

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