Variant report

Variant	rs1106240
Chromosome Location	chr12:123626982-123626983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123626633..123628310-chr12:123628394..123630305,2	MCF-7	breast:
2	chr12:123618954..123623520-chr12:123624080..123628885,6	MCF-7	breast:
3	chr12:123625936..123634145-chr12:123634916..123640513,10	K562	blood:
4	chr12:123625642..123631763-chr12:123633649..123636564,5	MCF-7	breast:
5	chr12:123623646..123628405-chr12:123632321..123637843,8	MCF-7	breast:
6	chr12:123623413..123625751-chr12:123625839..123628536,3	K562	blood:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1047158	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060105	0.89[CEU][hapmap];1.00[TSI][hapmap]
rs10732573	0.80[CEU][hapmap]
rs10744147	0.95[EUR][1000 genomes]
rs10772993	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.90[EUR][1000 genomes]
rs10772998	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10846478	0.90[EUR][1000 genomes]
rs10846486	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11057192	0.94[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs11057204	0.81[EUR][1000 genomes]
rs11057206	0.81[EUR][1000 genomes]
rs1106241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830103	0.84[CEU][hapmap]
rs12304248	0.89[CEU][hapmap]
rs12316131	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs12322888	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs1260294	0.94[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12817892	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12818067	0.83[EUR][1000 genomes]
rs12829456	0.83[EUR][1000 genomes]
rs1402274	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1463877	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs1533703	0.94[CEU][hapmap]
rs1569068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609520	0.80[CEU][hapmap]
rs1615350	0.89[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1615694	0.89[EUR][1000 genomes]
rs1616131	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1617434	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618679	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.89[EUR][1000 genomes]
rs1627724	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.89[EUR][1000 genomes]
rs1630905	0.90[EUR][1000 genomes]
rs1716156	0.86[EUR][1000 genomes]
rs1716157	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1716158	0.83[EUR][1000 genomes]
rs1716159	0.90[EUR][1000 genomes]
rs1716160	1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1716164	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1716165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716171	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716172	0.84[EUR][1000 genomes]
rs1716173	0.86[EUR][1000 genomes]
rs1716175	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1716176	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1716177	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1716182	0.89[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1716185	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727290	0.91[EUR][1000 genomes]
rs1727294	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1727296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.88[EUR][1000 genomes]
rs1727302	0.89[CEU][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1727306	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1727309	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1727310	0.92[EUR][1000 genomes]
rs1727313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727317	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.92[EUR][1000 genomes]
rs1727320	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1727322	0.88[EUR][1000 genomes]
rs1727323	1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1727324	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1727325	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1727331	0.80[CEU][hapmap]
rs1727334	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1790086	0.90[EUR][1000 genomes]
rs1790087	0.90[EUR][1000 genomes]
rs1790089	0.92[EUR][1000 genomes]
rs1790090	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790095	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1790098	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1790100	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1790101	0.89[EUR][1000 genomes]
rs1790102	0.89[EUR][1000 genomes]
rs1790108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790119	0.81[EUR][1000 genomes]
rs1790120	0.89[EUR][1000 genomes]
rs1790123	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1790124	0.87[EUR][1000 genomes]
rs1790125	0.82[EUR][1000 genomes]
rs1790130	0.89[EUR][1000 genomes]
rs1790131	1.00[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1879380	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs1969354	0.94[CEU][hapmap];0.91[TSI][hapmap]
rs1980252	0.94[CEU][hapmap]
rs2049114	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2337934	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs2510885	0.93[EUR][1000 genomes]
rs2682425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682429	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.89[EUR][1000 genomes]
rs2682431	0.91[EUR][1000 genomes]
rs2682433	0.93[EUR][1000 genomes]
rs2682434	1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2695476	0.93[EUR][1000 genomes]
rs2695478	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]
rs2695479	0.92[EUR][1000 genomes]
rs2695480	0.91[EUR][1000 genomes]
rs2695481	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.91[EUR][1000 genomes]
rs2851436	0.88[EUR][1000 genomes]
rs2851438	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.91[EUR][1000 genomes]
rs2851447	0.88[CEU][hapmap]
rs2851450	0.91[EUR][1000 genomes]
rs2851451	0.90[EUR][1000 genomes]
rs2947099	0.89[EUR][1000 genomes]
rs2950537	0.89[EUR][1000 genomes]
rs3018098	0.93[EUR][1000 genomes]
rs34341465	0.83[EUR][1000 genomes]
rs4372492	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4460848	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs4759371	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs4759409	0.94[CEU][hapmap]
rs4759415	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs520088	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs585522	0.86[TSI][hapmap]
rs58809476	0.83[EUR][1000 genomes]
rs641760	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs655293	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs7132277	0.89[CEU][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7299943	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs7304782	0.80[CEU][hapmap]
rs7313483	0.94[CEU][hapmap]
rs7953929	1.00[CEU][hapmap]
rs7980687	0.89[CEU][hapmap]
rs883263	0.88[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap]
rs884548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937564	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs941305	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs941306	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs949142	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795522	0.81[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1106240	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1106240	MPHOSPH9	cis	multi-tissue	Pritchard
rs1106240	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1106240	RILPL2	cis	lymphoblastoid	seeQTL
rs1106240	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1106240	CDK2AP1	cis	lymphoblastoid	seeQTL
rs1106240	OGFOD2	cis	brain	seeQTL
rs1106240	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1106240	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1106240	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1106240	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1106240	PITPNM2	cis	cerebellum	SCAN
rs1106240	ANAPC5	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr12:123624000-123627200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:123624000-123627200	Enhancers	HMEC	breast
5	chr12:123624000-123627400	Enhancers	Fetal Lung	lung
6	chr12:123624000-123627600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:123624000-123628000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:123624000-123628600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:123624000-123628600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr12:123624000-123628800	Enhancers	Brain Angular Gyrus	brain
11	chr12:123624000-123628800	Enhancers	Left Ventricle	heart
12	chr12:123624000-123629000	Enhancers	Colon Smooth Muscle	Colon
13	chr12:123624200-123627000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:123624200-123627000	Enhancers	Fetal Muscle Leg	muscle
15	chr12:123624200-123627000	Enhancers	NHEK	skin
16	chr12:123624200-123627200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr12:123624200-123627400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr12:123624200-123627400	Enhancers	Fetal Kidney	kidney
19	chr12:123624200-123627600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:123624200-123627600	Flanking Active TSS	HepG2	liver
21	chr12:123624200-123627800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr12:123624200-123627800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:123624200-123628000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:123624200-123628200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:123624200-123628200	Enhancers	Fetal Intestine Large	intestine
26	chr12:123624200-123628200	Enhancers	Fetal Intestine Small	intestine
27	chr12:123624200-123628200	Enhancers	Fetal Stomach	stomach
28	chr12:123624200-123628400	Enhancers	Placenta	Placenta
29	chr12:123624200-123628400	Enhancers	K562	blood
30	chr12:123624200-123628600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr12:123624200-123628800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:123624200-123629000	Enhancers	Brain Anterior Caudate	brain
33	chr12:123624200-123629000	Enhancers	Right Ventricle	heart
34	chr12:123624400-123627200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:123624400-123627200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:123624400-123627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:123624400-123627400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:123624400-123627400	Enhancers	HUVEC	blood vessel
39	chr12:123624400-123627600	Flanking Active TSS	Hela-S3	cervix
40	chr12:123624400-123627800	Enhancers	Stomach Mucosa	stomach
41	chr12:123624400-123628000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:123624400-123628600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:123624400-123628600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:123624400-123630400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr12:123624600-123627200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:123624600-123628000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:123624600-123628000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr12:123624600-123628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:123624600-123628200	Enhancers	Fetal Heart	heart
50	chr12:123624600-123628600	Enhancers	Adipose Nuclei	Adipose

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