Variant report

Variant	rs1609520
Chromosome Location	chr12:123735937-123735938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123735299-123736113	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:123734922-123736808	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:123735116-123736320	ECC-1	luminal epithelium:	n/a	n/a
4	SP1	chr12:123735161-123735964	A549	lung:	n/a	n/a
5	EP300	chr12:123735344-123735985	A549	lung:	n/a	n/a
6	MAX	chr12:123735256-123736035	MCF-7	breast:	n/a	n/a
7	TCF12	chr12:123734894-123736454	A549	lung:	n/a	n/a
8	RFX5	chr12:123735390-123735941	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:123735839-123737024	HepG2	liver:	n/a	n/a
10	FOSL2	chr12:123735161-123736019	A549	lung:	n/a	n/a
11	MAX	chr12:123735647-123736040	A549	lung:	n/a	n/a
12	POLR2A	chr12:123735764-123736068	K562	blood:	n/a	n/a
13	FOSL2	chr12:123735172-123736018	HepG2	liver:	n/a	n/a
14	BCL3	chr12:123734932-123736018	A549	lung:	n/a	n/a
15	TFAP2A	chr12:123735373-123735966	Hela-S3	cervix:	n/a	n/a
16	YY1	chr12:123735234-123735955	A549	lung:	n/a	n/a
17	POLR2A	chr12:123735329-123735975	Hela-S3	cervix:	n/a	n/a
18	MAX	chr12:123735272-123736155	A549	lung:	n/a	n/a
19	REST	chr12:123735122-123735948	A549	lung:	n/a	n/a
20	TFAP2C	chr12:123735322-123736042	Hela-S3	cervix:	n/a	chr12:123735789-123735804

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123464634..123466197-chr12:123735539..123737109,2	MCF-7	breast:
2	chr12:123451045..123452887-chr12:123735091..123736633,2	MCF-7	breast:
3	chr12:123715622..123719446-chr12:123735072..123738647,4	K562	blood:
4	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
5	chr12:123733810..123737382-chr12:123754694..123758405,4	MCF-7	breast:
6	chr12:123735647..123738456-chr12:123742871..123745926,3	K562	blood:
7	chr12:123735701..123738592-chr12:123744837..123746422,2	MCF-7	breast:
8	chr12:123735336..123737474-chr12:123737604..123739915,2	MCF-7	breast:
9	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:

No data

Variant related genes	Relation type
C12orf65	TF binding region
ENSG00000182196	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000235423	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10444439	0.82[JPT][hapmap]
rs1051431	0.80[CEU][hapmap]
rs1060105	0.85[GIH][hapmap]
rs10732573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10734901	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10744150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10744151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744152	0.94[JPT][hapmap]
rs10772997	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10772998	0.90[CEU][hapmap]
rs10772999	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773000	0.88[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10773002	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846486	0.80[CEU][hapmap]
rs10846489	0.91[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs10846517	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10846519	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10846520	0.88[JPT][hapmap]
rs10846523	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11057189	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11057202	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057204	0.80[EUR][1000 genomes]
rs11057205	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057206	0.81[EUR][1000 genomes]
rs11057207	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057209	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057210	0.82[EUR][1000 genomes]
rs11057223	0.83[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs11057287	0.94[JPT][hapmap]
rs1106240	0.80[CEU][hapmap]
rs1106241	0.80[CEU][hapmap]
rs1109559	0.91[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs1109560	0.83[JPT][hapmap]
rs11554169	0.97[ASN][1000 genomes]
rs12298826	0.85[GIH][hapmap]
rs12316131	0.85[GIH][hapmap]
rs12322888	0.85[GIH][hapmap]
rs1402274	0.80[CEU][hapmap]
rs1402275	0.84[GIH][hapmap]
rs1533703	0.83[CEU][hapmap]
rs1568427	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1568428	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1569068	0.80[CEU][hapmap]
rs1615350	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs1660	0.88[JPT][hapmap]
rs1716157	0.80[CEU][hapmap]
rs1716160	0.80[CEU][hapmap]
rs1716164	0.80[CEU][hapmap]
rs1716165	0.80[CEU][hapmap]
rs1716167	0.80[CEU][hapmap]
rs1716168	0.80[CEU][hapmap]
rs1716170	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs1716171	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs1716175	0.80[CEU][hapmap]
rs1716176	0.80[CEU][hapmap]
rs1716177	0.80[CEU][hapmap]
rs1727293	0.80[TSI][hapmap]
rs1727296	0.80[CEU][hapmap]
rs1727302	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs1727306	0.80[CEU][hapmap]
rs1727309	0.80[CEU][hapmap]
rs1727313	0.80[CEU][hapmap]
rs1727315	0.80[CEU][hapmap]
rs1727319	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727320	0.80[CEU][hapmap]
rs1727323	0.80[CEU][hapmap]
rs1727324	0.80[CEU][hapmap]
rs1727325	0.80[CEU][hapmap]
rs1727331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1727332	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1790095	0.80[CEU][hapmap]
rs1790098	0.80[CEU][hapmap]
rs1790100	0.80[CEU][hapmap]
rs1790108	0.80[CEU][hapmap]
rs1790123	0.80[CEU][hapmap]
rs1790131	0.80[CEU][hapmap]
rs1879379	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1879380	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs1969354	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs1969355	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1980251	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980252	0.85[CEU][hapmap]
rs2049114	0.80[CEU][hapmap]
rs2090764	0.99[ASN][1000 genomes]
rs2102949	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271976	0.84[JPT][hapmap]
rs2280424	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2337934	0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs2682434	0.80[CEU][hapmap]
rs2695478	0.80[CEU][hapmap]
rs2695482	0.80[CEU][hapmap]
rs28362667	0.84[ASN][1000 genomes]
rs28362669	0.82[ASN][1000 genomes]
rs28406193	0.85[GIH][hapmap]
rs28414347	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs28458312	0.85[GIH][hapmap]
rs28472704	0.85[GIH][hapmap]
rs28501453	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2851443	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2851447	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28587386	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs28595660	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs28613486	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs28636834	0.85[GIH][hapmap]
rs36121382	0.82[ASN][1000 genomes]
rs3759111	0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3759113	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs3759114	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3803001	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3825141	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4268544	0.83[EUR][1000 genomes]
rs4372492	0.80[CEU][hapmap]
rs4460848	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4474478	0.95[ASN][1000 genomes]
rs4474479	0.95[ASN][1000 genomes]
rs4594040	0.95[ASN][1000 genomes]
rs4759367	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4759371	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs4759372	0.96[ASN][1000 genomes]
rs4759407	0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4759408	0.84[ASN][1000 genomes]
rs4759409	0.85[CEU][hapmap]
rs4759411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4759413	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4759414	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4759415	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs4759418	0.89[ASN][1000 genomes]
rs57676984	0.84[ASN][1000 genomes]
rs60077920	0.84[ASN][1000 genomes]
rs60254089	0.94[ASN][1000 genomes]
rs61231969	0.89[ASN][1000 genomes]
rs61519741	0.93[ASN][1000 genomes]
rs7137286	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139321	0.84[JPT][hapmap]
rs7297649	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7304782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313483	0.90[CEU][hapmap]
rs7953929	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs7959415	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs884548	0.80[CEU][hapmap]
rs941305	0.80[CEU][hapmap]
rs941306	0.80[CEU][hapmap]
rs9795522	0.81[EUR][1000 genomes]
rs9795593	0.85[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers 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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1609520	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1609520	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1609520	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1609520	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1609520	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1609520	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1609520	OGFOD2	cis	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
2	chr12:123719600-123738400	Weak transcription	NH-A	brain
3	chr12:123720000-123736000	Weak transcription	Gastric	stomach
4	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
5	chr12:123725200-123738000	Weak transcription	HSMM	muscle
6	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:123727400-123736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:123727400-123738000	Weak transcription	NHDF-Ad	bronchial
9	chr12:123727400-123738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:123727600-123736400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:123727600-123738000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:123727600-123738000	Weak transcription	HUVEC	blood vessel
13	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:123727800-123738200	Weak transcription	Fetal Heart	heart
15	chr12:123732000-123738200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:123732800-123737000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:123733200-123736800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:123733400-123736400	Weak transcription	Fetal Lung	lung
19	chr12:123733400-123736400	Weak transcription	NHLF	lung
20	chr12:123733400-123738000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:123733400-123738000	Weak transcription	Primary B cells from cord blood	blood
22	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:123733600-123736800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:123733800-123738000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:123734000-123736400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr12:123734000-123737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:123734000-123738400	Weak transcription	Osteobl	bone
28	chr12:123734200-123736400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:123734200-123737800	Weak transcription	GM12878-XiMat	blood
30	chr12:123734200-123738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:123734400-123736000	Weak transcription	Dnd41	blood
32	chr12:123734400-123738400	Weak transcription	Aorta	Aorta
33	chr12:123734400-123738600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:123734800-123737000	Enhancers	Esophagus	oesophagus
36	chr12:123735000-123736000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:123735000-123736000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:123735000-123736000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:123735000-123736200	Enhancers	Liver	Liver
40	chr12:123735000-123736200	Genic enhancers	Fetal Thymus	thymus
41	chr12:123735000-123736200	Transcr. at gene 5' and 3'	A549	lung
42	chr12:123735000-123736200	Flanking Active TSS	Hela-S3	cervix
43	chr12:123735000-123736400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:123735000-123736600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:123735000-123736600	Enhancers	Fetal Intestine Large	intestine
46	chr12:123735000-123736600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr12:123735000-123736600	Enhancers	HMEC	breast
48	chr12:123735000-123736800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:123735000-123737000	Enhancers	Brain Substantia Nigra	brain
50	chr12:123735000-123737000	Genic enhancers	Fetal Intestine Small	intestine

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