Variant report

Variant	rs655293
Chromosome Location	chr12:123528405-123528406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123527734..123528656-chr12:123722305..123723382,7	MCF-7	breast:
2	chr12:123521446..123523784-chr12:123527111..123528952,2	K562	blood:
3	chr12:123527949..123530263-chr12:124116742..124119080,2	MCF-7	breast:
4	chr12:123527736..123529546-chr12:123540101..123542162,2	K562	blood:
5	chr12:123527749..123528657-chr12:123633701..123634611,3	MCF-7	breast:
6	chr12:123527755..123528597-chr12:123722388..123723377,4	MCF-7	breast:
7	chr12:123527304..123529634-chr12:123630952..123633326,2	MCF-7	breast:
8	chr12:123527678..123528658-chr12:123634881..123635709,3	MCF-7	breast:
9	chr12:123525729..123528577-chr12:123717047..123721067,3	MCF-7	breast:
10	chr12:123527596..123531182-chr12:123539339..123542162,4	K562	blood:
11	chr12:123519670..123521878-chr12:123527130..123529862,2	MCF-7	breast:
12	chr12:123526656..123529148-chr12:123634939..123636869,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1051431	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs10772998	0.89[CEU][hapmap]
rs10846486	0.94[CEU][hapmap]
rs11057192	0.89[CEU][hapmap];0.97[TSI][hapmap]
rs1106240	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs1106241	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1260294	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12811109	0.88[EUR][1000 genomes]
rs12820906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12828755	0.87[EUR][1000 genomes]
rs1402274	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1463877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1569068	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1615350	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1617156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716157	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1716160	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716164	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1716165	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716167	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1716168	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1716171	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1716175	0.94[CEU][hapmap]
rs1716176	0.94[CEU][hapmap]
rs1716177	0.94[CEU][hapmap]
rs1727294	0.93[CEU][hapmap];0.93[ASN][1000 genomes]
rs1727296	0.94[CEU][hapmap]
rs1727302	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1727306	0.94[CEU][hapmap]
rs1727309	0.94[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1727313	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1727315	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1727320	0.94[CEU][hapmap]
rs1727323	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1727324	0.94[CEU][hapmap]
rs1727325	0.94[CEU][hapmap]
rs1727334	0.86[CEU][hapmap]
rs1790095	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1790098	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1790100	0.94[CEU][hapmap]
rs1790108	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1790116	0.88[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1790119	0.81[ASN][1000 genomes]
rs1790120	0.89[ASN][1000 genomes]
rs1790123	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1790131	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2049114	0.94[CEU][hapmap]
rs2270789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2510885	0.93[ASN][1000 genomes]
rs2682434	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2695478	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs2695482	0.94[CEU][hapmap]
rs2851447	0.82[CEU][hapmap]
rs4148856	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4372492	0.94[CEU][hapmap]
rs4460848	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4759409	0.89[CEU][hapmap]
rs520088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585522	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[LWK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs641760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs7132277	0.94[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs71444568	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7296418	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7299943	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7313483	0.89[CEU][hapmap]
rs7975763	0.85[ASN][1000 genomes]
rs883263	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883563	0.86[EUR][1000 genomes]
rs884548	0.94[CEU][hapmap]
rs937564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs940904	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs941305	0.94[CEU][hapmap]
rs941306	0.94[CEU][hapmap]

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	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	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
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs655293	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs655293	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs655293	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs655293	CDK2AP1	cis	multi-tissue	Pritchard
rs655293	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs655293	CCDC92	cis	cerebellum	SCAN
rs655293	HIP1R	cis	parietal	SCAN
rs655293	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs655293	PITPNM2	cis	cerebellum	SCAN
rs655293	CDK2AP1	cis	lymphoblastoid	seeQTL
rs655293	ANAPC5	cis	parietal	SCAN
rs655293	TMEM120B	cis	parietal	SCAN
rs655293	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs655293	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs655293	LOC283378	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123497400-123528600	Weak transcription	Ovary	ovary
2	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
3	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:123518200-123535600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:123518400-123533600	Weak transcription	Aorta	Aorta
6	chr12:123518800-123540600	Weak transcription	HepG2	liver
7	chr12:123519000-123540400	Weak transcription	Gastric	stomach
8	chr12:123519000-123543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:123525400-123529400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:123525400-123530000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:123526000-123529800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
12	chr12:123526000-123531000	Enhancers	Placenta	Placenta
13	chr12:123526000-123531400	Enhancers	Colon Smooth Muscle	Colon
14	chr12:123526400-123529000	Enhancers	Fetal Muscle Trunk	muscle
15	chr12:123526400-123529200	Enhancers	NHLF	lung
16	chr12:123526400-123530400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:123526400-123530800	Enhancers	Fetal Muscle Leg	muscle
18	chr12:123526400-123531000	Enhancers	Brain Cingulate Gyrus	brain
19	chr12:123526400-123531000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr12:123526400-123531600	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:123526600-123528800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr12:123526600-123528800	Enhancers	Fetal Intestine Large	intestine
23	chr12:123526600-123530800	Enhancers	Left Ventricle	heart
24	chr12:123526600-123531200	Enhancers	Right Atrium	heart
25	chr12:123526800-123530600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:123526800-123531200	Enhancers	Fetal Heart	heart
27	chr12:123527200-123529200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:123527200-123529200	Enhancers	Primary hematopoietic stem cells	blood
29	chr12:123527200-123529200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:123527200-123529800	Enhancers	Liver	Liver
31	chr12:123527400-123529000	Enhancers	Duodenum Mucosa	Duodenum
32	chr12:123527400-123529000	Enhancers	Fetal Intestine Small	intestine
33	chr12:123527400-123529200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:123527400-123529400	Enhancers	Brain Hippocampus Middle	brain
35	chr12:123527400-123529400	Enhancers	Small Intestine	intestine
36	chr12:123527400-123530800	Enhancers	Colonic Mucosa	Colon
37	chr12:123527400-123531400	Enhancers	Fetal Stomach	stomach
38	chr12:123527600-123528800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:123527600-123529200	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr12:123527600-123529600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:123527600-123529800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr12:123527600-123530200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:123527800-123528600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:123527800-123528800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr12:123527800-123528800	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:123527800-123528800	Enhancers	Dnd41	blood
47	chr12:123527800-123529000	Enhancers	Stomach Mucosa	stomach
48	chr12:123527800-123529000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr12:123527800-123529000	Enhancers	NH-A	brain
50	chr12:123527800-123529200	Enhancers	HUES6 Cell Line	embryonic stem cell

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