Variant report

Variant	rs2947099
Chromosome Location	chr12:123674251-123674252
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	chr12:123636212..123638464-chr12:123674064..123676672,2	K562	blood:
2	chr12:123673846..123675377-chr12:123716502..123718464,2	K562	blood:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1047158	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1051431	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10744147	0.88[EUR][1000 genomes]
rs10744148	0.83[EUR][1000 genomes]
rs10744149	0.84[AMR][1000 genomes]
rs10772993	0.89[EUR][1000 genomes]
rs10772995	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10772996	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10772998	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10846478	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846486	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10846487	0.83[EUR][1000 genomes]
rs11057189	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11057192	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11057204	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11057206	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11057210	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1106240	0.89[EUR][1000 genomes]
rs1106241	0.91[EUR][1000 genomes]
rs12817892	0.83[EUR][1000 genomes]
rs12818067	0.83[EUR][1000 genomes]
rs12829456	0.83[EUR][1000 genomes]
rs1402274	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1569068	0.90[EUR][1000 genomes]
rs1615694	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1616131	0.90[EUR][1000 genomes]
rs1616181	0.90[EUR][1000 genomes]
rs1617156	0.84[EUR][1000 genomes]
rs1617434	0.91[EUR][1000 genomes]
rs1618679	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1621194	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1626899	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1627724	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1630693	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1630905	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716156	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716157	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716158	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716159	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716160	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1716164	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716165	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716167	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716168	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716170	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716171	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716172	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716173	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716175	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716176	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716177	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716182	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716185	0.89[EUR][1000 genomes]
rs1727290	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1727294	0.90[EUR][1000 genomes]
rs1727296	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727300	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1727306	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727309	0.92[EUR][1000 genomes]
rs1727310	0.92[EUR][1000 genomes]
rs1727313	0.88[EUR][1000 genomes]
rs1727314	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727315	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727316	0.90[EUR][1000 genomes]
rs1727317	0.87[EUR][1000 genomes]
rs1727318	0.86[EUR][1000 genomes]
rs1727320	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1727322	0.88[EUR][1000 genomes]
rs1727323	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1727324	0.92[EUR][1000 genomes]
rs1727325	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1727334	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790086	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1790087	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1790089	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790090	0.91[EUR][1000 genomes]
rs1790095	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790098	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790099	0.94[AFR][1000 genomes]
rs1790100	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790101	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1790102	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1790108	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1790109	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1790116	0.90[EUR][1000 genomes]
rs1790120	0.81[EUR][1000 genomes]
rs1790123	0.92[EUR][1000 genomes]
rs1790124	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1790125	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790130	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1790131	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2049114	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2102949	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2510885	0.87[EUR][1000 genomes]
rs2682425	0.81[EUR][1000 genomes]
rs2682429	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682430	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682431	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682433	0.93[EUR][1000 genomes]
rs2682434	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2695476	0.93[EUR][1000 genomes]
rs2695478	0.94[EUR][1000 genomes]
rs2695479	0.92[EUR][1000 genomes]
rs2695480	0.91[EUR][1000 genomes]
rs2695481	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2695482	0.91[EUR][1000 genomes]
rs2851435	0.91[EUR][1000 genomes]
rs2851436	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851438	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2851441	0.86[EUR][1000 genomes]
rs2851443	0.80[EUR][1000 genomes]
rs2851447	0.81[EUR][1000 genomes]
rs2851450	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2851451	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2950537	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3018098	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34341465	0.83[EUR][1000 genomes]
rs4372492	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4460848	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4759409	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58809476	0.83[EUR][1000 genomes]
rs7313483	0.83[EUR][1000 genomes]
rs884548	0.91[EUR][1000 genomes]
rs941305	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs941306	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949142	0.91[EUR][1000 genomes]
rs9795522	0.84[AMR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2947099	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs2947099	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs2947099	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs2947099	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs2947099	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs2947099	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs2947099	ABCB9	cis	Skin Sun Exposed Lower leg	GTEx
rs2947099	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs2947099	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123676200	Weak transcription	Gastric	stomach
2	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
3	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
4	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
5	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
6	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
10	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
12	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
14	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
15	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:123651400-123675800	Weak transcription	Ovary	ovary
17	chr12:123651600-123676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:123652200-123676200	Weak transcription	Right Ventricle	heart
19	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:123654600-123683000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:123655000-123681000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:123655200-123682200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:123657000-123680600	Strong transcription	Fetal Stomach	stomach
30	chr12:123657000-123680800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:123658600-123682000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:123658800-123675800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:123659800-123675200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:123661400-123687200	Weak transcription	Fetal Brain Male	brain
35	chr12:123663200-123677800	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:123664200-123678000	Weak transcription	Fetal Kidney	kidney
37	chr12:123664600-123675200	Weak transcription	Placenta	Placenta
38	chr12:123665000-123685800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:123665800-123703800	Weak transcription	Stomach Mucosa	stomach
40	chr12:123666200-123675200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:123666200-123676000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:123666200-123676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:123666400-123674600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:123667600-123695000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:123667800-123682000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:123668200-123680000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:123668200-123680200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:123668200-123682000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:123668200-123682000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:123668200-123703600	Strong transcription	Primary monocytes fromperipheralblood	blood

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