Variant report

Variant	rs1617434
Chromosome Location	chr12:123649486-123649487
allele	C/T
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	MAFK	chr12:123649467-123649736	HepG2	liver:	n/a	n/a
2	MAFK	chr12:123649424-123649755	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123634053..123636860-chr12:123645111..123649875,5	MCF-7	breast:

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

Extended variants
information (count: 131 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1047158	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10772993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.92[EUR][1000 genomes]
rs10772998	0.83[EUR][1000 genomes]
rs10846478	0.92[EUR][1000 genomes]
rs10846486	0.89[EUR][1000 genomes]
rs10846487	0.81[EUR][1000 genomes]
rs11057192	0.93[EUR][1000 genomes]
rs11057204	0.82[EUR][1000 genomes]
rs11057206	0.83[EUR][1000 genomes]
rs11057210	0.82[EUR][1000 genomes]
rs1106240	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106241	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260294	0.86[EUR][1000 genomes]
rs12817892	0.85[EUR][1000 genomes]
rs12818067	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12829456	0.85[EUR][1000 genomes]
rs1402274	0.94[EUR][1000 genomes]
rs1569068	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615350	0.83[EUR][1000 genomes]
rs1615694	0.91[EUR][1000 genomes]
rs1616131	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.87[EUR][1000 genomes]
rs1618679	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.91[EUR][1000 genomes]
rs1627724	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.91[EUR][1000 genomes]
rs1630905	0.92[EUR][1000 genomes]
rs1716156	0.88[EUR][1000 genomes]
rs1716157	0.92[EUR][1000 genomes]
rs1716158	0.85[EUR][1000 genomes]
rs1716159	0.92[EUR][1000 genomes]
rs1716160	0.93[EUR][1000 genomes]
rs1716164	0.90[EUR][1000 genomes]
rs1716165	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	0.85[EUR][1000 genomes]
rs1716171	0.85[EUR][1000 genomes]
rs1716172	0.86[EUR][1000 genomes]
rs1716173	0.88[EUR][1000 genomes]
rs1716175	0.92[EUR][1000 genomes]
rs1716176	0.95[EUR][1000 genomes]
rs1716177	0.95[EUR][1000 genomes]
rs1716182	0.91[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1716185	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727290	0.93[EUR][1000 genomes]
rs1727294	0.95[EUR][1000 genomes]
rs1727296	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.90[EUR][1000 genomes]
rs1727302	0.81[EUR][1000 genomes]
rs1727306	0.92[EUR][1000 genomes]
rs1727309	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727310	0.94[EUR][1000 genomes]
rs1727313	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727317	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.91[EUR][1000 genomes]
rs1727320	0.93[EUR][1000 genomes]
rs1727322	0.90[EUR][1000 genomes]
rs1727323	0.93[EUR][1000 genomes]
rs1727324	0.94[EUR][1000 genomes]
rs1727325	0.93[EUR][1000 genomes]
rs1727334	0.85[EUR][1000 genomes]
rs1790086	0.92[EUR][1000 genomes]
rs1790087	0.92[EUR][1000 genomes]
rs1790089	0.94[EUR][1000 genomes]
rs1790090	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790095	0.94[EUR][1000 genomes]
rs1790098	0.95[EUR][1000 genomes]
rs1790100	0.94[EUR][1000 genomes]
rs1790101	0.91[EUR][1000 genomes]
rs1790102	0.91[EUR][1000 genomes]
rs1790108	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790120	0.88[EUR][1000 genomes]
rs1790123	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1790124	0.89[EUR][1000 genomes]
rs1790125	0.84[EUR][1000 genomes]
rs1790130	0.91[EUR][1000 genomes]
rs1790131	0.92[EUR][1000 genomes]
rs2049114	0.92[EUR][1000 genomes]
rs2510885	0.92[EUR][1000 genomes]
rs2682425	0.88[EUR][1000 genomes]
rs2682429	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.91[EUR][1000 genomes]
rs2682431	0.93[EUR][1000 genomes]
rs2682433	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682434	0.93[EUR][1000 genomes]
rs2695476	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2695478	0.96[EUR][1000 genomes]
rs2695479	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2695480	0.93[EUR][1000 genomes]
rs2695481	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851436	0.90[EUR][1000 genomes]
rs2851438	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.90[EUR][1000 genomes]
rs2851450	0.93[EUR][1000 genomes]
rs2851451	0.92[EUR][1000 genomes]
rs2947099	0.91[EUR][1000 genomes]
rs2950537	0.91[EUR][1000 genomes]
rs3018098	0.95[EUR][1000 genomes]
rs34341465	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4372492	0.93[EUR][1000 genomes]
rs4759409	0.81[EUR][1000 genomes]
rs58809476	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7313483	0.81[EUR][1000 genomes]
rs884548	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941305	0.85[EUR][1000 genomes]
rs941306	0.85[EUR][1000 genomes]
rs949142	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795522	0.83[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1617434	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1617434	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1617434	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1617434	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1617434	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1617434	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1617434	CDK2AP1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636400-123649800	Weak transcription	Ovary	ovary
2	chr12:123636400-123650200	Weak transcription	Aorta	Aorta
3	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:123636600-123676200	Weak transcription	Gastric	stomach
5	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
6	chr12:123636800-123650200	Weak transcription	Brain Substantia Nigra	brain
7	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
8	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
9	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
10	chr12:123637000-123650000	Weak transcription	Lung	lung
11	chr12:123637000-123650000	Weak transcription	Spleen	Spleen
12	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:123638000-123652400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:123638000-123652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:123638200-123652400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:123638200-123652800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:123638600-123650400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
22	chr12:123640200-123652800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:123640600-123657800	Weak transcription	NHLF	lung
25	chr12:123643000-123651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:123643000-123652800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:123643000-123652800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:123643000-123652800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:123643200-123651800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:123643200-123652000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:123643200-123652600	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:123643400-123651800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:123643400-123652400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr12:123643600-123651600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:123643600-123652600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:123643800-123652400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr12:123643800-123652600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:123644000-123650800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:123644000-123651600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:123644000-123652400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:123644000-123652800	Strong transcription	Dnd41	blood
42	chr12:123644200-123650600	Strong transcription	HSMM	muscle
43	chr12:123644400-123650000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:123644600-123653000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr12:123644800-123651800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:123645000-123650000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:123645000-123650800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:123645000-123651400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:123645000-123652800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:123645200-123651200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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