Variant report

Variant	rs1727293
Chromosome Location	chr12:123648032-123648033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL1	chr12:123647790-123648196	HCT-116	colon:	n/a	chr12:123647897-123647908

No.	Distal block	Cell Line	Cell type
1	chr12:123637836..123642861-chr12:123644495..123649304,6	MCF-7	breast:
2	chr12:123646433..123649058-chr12:123716040..123717583,2	MCF-7	breast:
3	chr12:123639375..123642354-chr12:123646005..123648367,2	K562	blood:
4	chr12:123634053..123636860-chr12:123645111..123649875,5	MCF-7	breast:

Variant related genes	Relation type
MPHOSPH9	TF binding region
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10444439	0.81[JPT][hapmap]
rs1051434	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773000	0.80[GIH][hapmap];0.84[JPT][hapmap]
rs10773002	0.83[ASW][hapmap]
rs10773003	0.90[JPT][hapmap]
rs10773005	0.90[JPT][hapmap]
rs10773921	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10846489	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10848428	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057219	0.82[AFR][1000 genomes]
rs11057223	0.84[JPT][hapmap]
rs11057251	0.90[ASW][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs11057276	1.00[ASW][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs1109559	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1109560	0.83[JPT][hapmap]
rs11608305	0.90[JPT][hapmap]
rs11608811	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11610710	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11613128	0.87[AFR][1000 genomes]
rs12229700	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12317452	0.90[JPT][hapmap]
rs12366872	0.90[JPT][hapmap]
rs12425009	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12425850	1.00[YRI][hapmap]
rs1568427	0.83[ASW][hapmap]
rs1568428	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1609520	0.80[TSI][hapmap]
rs1611973	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1615350	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1616484	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1626703	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1716178	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716184	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727286	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1727295	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727301	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1727302	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727305	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727307	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1727312	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790088	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1790094	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790096	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790104	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790106	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790121	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790122	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790129	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790134	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879379	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2271976	0.84[JPT][hapmap]
rs2337630	0.82[AFR][1000 genomes]
rs2337631	0.82[AFR][1000 genomes]
rs2682427	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3088303	0.90[JPT][hapmap]
rs34841857	0.82[AFR][1000 genomes]
rs3741530	0.96[CEU][hapmap]
rs3759115	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3897102	0.91[CHB][hapmap]
rs4148862	0.87[EUR][1000 genomes]
rs4148863	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4460848	0.83[TSI][hapmap]
rs4553407	0.82[AFR][1000 genomes]
rs4759377	0.90[JPT][hapmap]
rs58991895	0.82[ASN][1000 genomes]
rs61041384	0.83[ASN][1000 genomes]
rs61187102	0.82[ASN][1000 genomes]
rs7135296	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7139321	0.81[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7296418	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[TSI][hapmap]
rs7304782	0.83[ASW][hapmap]
rs7305511	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7315453	0.90[JPT][hapmap]
rs7957096	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap]
rs7972811	0.90[JPT][hapmap]
rs884956	1.00[ASW][hapmap];0.86[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs949143	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	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
9	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1727293	ANAPC5	cis	parietal	SCAN
rs1727293	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1727293	TMEM120B	cis	parietal	SCAN
rs1727293	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727293	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1727293	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727293	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727293	IL31	cis	parietal	SCAN
rs1727293	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1727293	PITPNM2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636400-123649000	Weak transcription	Small Intestine	intestine
2	chr12:123636400-123649200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:123636400-123649800	Weak transcription	Ovary	ovary
4	chr12:123636400-123650200	Weak transcription	Aorta	Aorta
5	chr12:123636600-123648400	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:123636600-123648400	Weak transcription	HSMMtube	muscle
7	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:123636600-123676200	Weak transcription	Gastric	stomach
9	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
10	chr12:123636800-123649000	Weak transcription	Right Ventricle	heart
11	chr12:123636800-123649200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:123636800-123649200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:123636800-123650200	Weak transcription	Brain Substantia Nigra	brain
14	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
15	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
16	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
17	chr12:123637000-123648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:123637000-123648400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:123637000-123648400	Weak transcription	Primary B cells from cord blood	blood
20	chr12:123637000-123648600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:123637000-123649200	Weak transcription	Pancreas	Pancrea
22	chr12:123637000-123650000	Weak transcription	Lung	lung
23	chr12:123637000-123650000	Weak transcription	Spleen	Spleen
24	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:123637200-123648600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:123637600-123648600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:123637800-123648200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:123638000-123648400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:123638000-123652400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:123638000-123652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:123638200-123652400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:123638200-123652800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:123638600-123650400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
38	chr12:123640200-123652800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:123640600-123648400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:123640600-123648400	Weak transcription	Left Ventricle	heart
42	chr12:123640600-123657800	Weak transcription	NHLF	lung
43	chr12:123641800-123648400	Weak transcription	HUVEC	blood vessel
44	chr12:123641800-123648400	Weak transcription	Osteobl	bone
45	chr12:123643000-123651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:123643000-123652800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:123643000-123652800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:123643000-123652800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:123643200-123651800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:123643200-123652000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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