Variant report

Variant	rs1260294
Chromosome Location	chr12:123560289-123560290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123558728..123560764-chr12:123563794..123566553,2	MCF-7	breast:
2	chr12:123557772..123560593-chr12:123574740..123576717,2	K562	blood:
3	chr12:123559703..123562585-chr12:123566918..123569407,2	K562	blood:
4	chr12:123463143..123466030-chr12:123559790..123563075,3	MCF-7	breast:
5	chr12:123558968..123563276-chr12:123716606..123719909,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251497	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1047158	0.86[EUR][1000 genomes]
rs1051431	0.94[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10744147	0.84[EUR][1000 genomes]
rs10772993	0.85[EUR][1000 genomes]
rs10772995	0.80[EUR][1000 genomes]
rs10772998	0.89[CEU][hapmap]
rs10846478	0.80[EUR][1000 genomes]
rs10846486	0.94[CEU][hapmap]
rs11057192	0.89[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1106240	0.94[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1106241	0.94[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs12811109	0.80[EUR][1000 genomes]
rs12817892	0.91[CEU][hapmap]
rs1402274	0.94[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1402275	0.84[GIH][hapmap]
rs1463877	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1533703	0.88[CEU][hapmap]
rs1569068	0.94[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1615350	0.84[CEU][hapmap]
rs1616131	0.87[EUR][1000 genomes]
rs1616181	0.87[EUR][1000 genomes]
rs1617156	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1617434	0.86[EUR][1000 genomes]
rs1618679	0.81[EUR][1000 genomes]
rs1621194	0.84[EUR][1000 genomes]
rs1627724	0.86[EUR][1000 genomes]
rs1630905	0.80[EUR][1000 genomes]
rs1716157	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs1716159	0.80[EUR][1000 genomes]
rs1716160	0.94[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1716164	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs1716165	0.94[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1716167	0.94[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1716168	0.94[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1716170	0.94[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs1716171	0.94[CEU][hapmap];0.91[TSI][hapmap]
rs1716175	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1716176	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1716177	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1716185	0.83[EUR][1000 genomes]
rs1727290	0.83[EUR][1000 genomes]
rs1727294	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs1727296	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs1727302	0.84[CEU][hapmap]
rs1727306	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs1727309	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1727310	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1727313	0.94[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1727314	0.84[EUR][1000 genomes]
rs1727315	0.94[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1727316	0.87[EUR][1000 genomes]
rs1727317	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727318	0.81[EUR][1000 genomes]
rs1727320	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1727323	0.94[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1727324	0.94[CEU][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1727325	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1727334	0.86[CEU][hapmap]
rs1790086	0.80[EUR][1000 genomes]
rs1790087	0.80[EUR][1000 genomes]
rs1790089	0.82[EUR][1000 genomes]
rs1790090	0.86[EUR][1000 genomes]
rs1790095	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1790098	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1790100	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs1790108	0.94[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1790109	0.86[EUR][1000 genomes]
rs1790116	0.88[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1790120	0.86[EUR][1000 genomes]
rs1790123	0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1790131	0.94[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs1879380	0.94[CEU][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs1969354	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1980252	0.89[CEU][hapmap]
rs2049114	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs2337934	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2510885	0.87[EUR][1000 genomes]
rs2682429	0.86[EUR][1000 genomes]
rs2682431	0.81[EUR][1000 genomes]
rs2682433	0.83[EUR][1000 genomes]
rs2682434	0.94[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2695476	0.83[EUR][1000 genomes]
rs2695478	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]
rs2695479	0.82[EUR][1000 genomes]
rs2695480	0.81[EUR][1000 genomes]
rs2695481	0.86[EUR][1000 genomes]
rs2695482	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2851435	0.81[EUR][1000 genomes]
rs2851438	0.86[EUR][1000 genomes]
rs2851441	0.82[EUR][1000 genomes]
rs2851447	0.82[CEU][hapmap]
rs2851450	0.81[EUR][1000 genomes]
rs2851451	0.80[EUR][1000 genomes]
rs3018098	0.83[EUR][1000 genomes]
rs4372492	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4460848	0.84[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs4759371	0.89[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs4759409	0.89[CEU][hapmap]
rs4759415	0.89[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs520088	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs585522	0.84[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs641760	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs655293	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7132277	0.84[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71444568	0.87[EUR][1000 genomes]
rs7299943	0.94[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7313483	0.89[CEU][hapmap]
rs7953929	0.94[CEU][hapmap]
rs883263	0.94[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs884548	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs937564	1.00[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs941305	0.94[CEU][hapmap]
rs941306	0.94[CEU][hapmap]
rs949142	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	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
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	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
10	esv3421941	chr12:123556899-123561197	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1260294	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1260294	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1260294	CDK2AP1	cis	lymphoblastoid	seeQTL
rs1260294	TMEM120B	cis	parietal	SCAN
rs1260294	HIP1R	cis	parietal	SCAN
rs1260294	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1260294	ANAPC5	cis	parietal	SCAN
rs1260294	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1260294	PITPNM2	cis	cerebellum	SCAN
rs1260294	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1260294	CCDC92	cis	cerebellum	SCAN
rs1260294	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1260294	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1260294	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
2	chr12:123546400-123562400	Enhancers	Liver	Liver
3	chr12:123549600-123561000	Weak transcription	Hela-S3	cervix
4	chr12:123550000-123562400	Enhancers	Fetal Heart	heart
5	chr12:123551200-123560400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:123551200-123561800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:123553800-123563800	Enhancers	Right Ventricle	heart
8	chr12:123554000-123563000	Enhancers	Right Atrium	heart
9	chr12:123554000-123563800	Enhancers	Brain Hippocampus Middle	brain
10	chr12:123554400-123560400	Enhancers	Colon Smooth Muscle	Colon
11	chr12:123555600-123561200	Weak transcription	Pancreas	Pancrea
12	chr12:123555800-123560800	Weak transcription	HUVEC	blood vessel
13	chr12:123555800-123561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:123556400-123561200	Weak transcription	NHLF	lung
15	chr12:123556400-123562600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:123556600-123561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:123557400-123565600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:123557600-123560400	Enhancers	Brain Anterior Caudate	brain
19	chr12:123557800-123561400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:123558000-123560800	Enhancers	Brain Substantia Nigra	brain
21	chr12:123558400-123561400	Enhancers	Brain Cingulate Gyrus	brain
22	chr12:123558400-123563800	Enhancers	Lung	lung
23	chr12:123558600-123561600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr12:123558600-123562400	Enhancers	Adipose Nuclei	Adipose
25	chr12:123558600-123562800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:123558800-123561600	Enhancers	Fetal Muscle Leg	muscle
27	chr12:123558800-123563200	Flanking Active TSS	Fetal Brain Female	brain
28	chr12:123559000-123560400	Enhancers	Primary B cells from cord blood	blood
29	chr12:123559000-123560600	Enhancers	Esophagus	oesophagus
30	chr12:123559000-123561000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:123559000-123561000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:123559000-123561000	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr12:123559000-123561400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:123559000-123561600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:123559000-123561600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr12:123559000-123561800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr12:123559000-123562000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:123559200-123560800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:123559200-123561400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:123559200-123561600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr12:123559200-123561600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:123559200-123561800	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:123559200-123562000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr12:123559200-123562200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr12:123559400-123560400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:123559400-123560600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:123559400-123561000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:123559400-123561400	Enhancers	Fetal Lung	lung
49	chr12:123559400-123561400	Enhancers	HSMMtube	muscle
50	chr12:123559400-123561600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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