Variant report

Variant	rs12067685
Chromosome Location	chr1:150952917-150952918
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150951645..150956254-chr1:150963775..150970753,11	MCF-7	breast:
2	chr1:150951870..150954741-chr1:151030040..151032027,2	K562	blood:
3	chr1:150898177..150900338-chr1:150951575..150953593,2	MCF-7	breast:
4	chr1:150533509..150537383-chr1:150951108..150953934,3	K562	blood:
5	chr1:150951620..150955085-chr1:150979651..150983018,4	K562	blood:
6	chr1:150951084..150953153-chr1:150955362..150957239,2	K562	blood:
7	chr1:150950075..150953840-chr1:150979246..150981801,5	K562	blood:
8	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
9	chr1:150549116..150552105-chr1:150952338..150954284,2	MCF-7	breast:
10	chr1:150950114..150953759-chr1:150976393..150978885,3	K562	blood:
11	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
12	chr1:150835862..150838203-chr1:150950221..150953041,2	K562	blood:
13	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
14	chr1:150748050..150749658-chr1:150951794..150953371,2	K562	blood:
15	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
16	chr1:150952576..150954333-chr7:75931969..75934548,2	MCF-7	breast:
17	chr1:149856818..149859748-chr1:150952737..150955704,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000106211	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10399947	0.80[EUR][1000 genomes]
rs10888397	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888398	0.82[ASN][1000 genomes]
rs11204739	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11204742	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204743	0.84[ASN][1000 genomes]
rs11204747	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204748	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204749	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204750	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579736	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581757	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583707	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589886	0.82[ASN][1000 genomes]
rs12059949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12090215	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12096831	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12097963	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12405726	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12409208	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12410394	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12562939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546376	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972060	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2004903	0.87[ASN][1000 genomes]
rs2124952	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271076	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272214	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280627	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864882	0.82[ASN][1000 genomes]
rs2867296	0.84[EUR][1000 genomes]
rs34985895	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3843843	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3849279	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4451553	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970928	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970929	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970930	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970931	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4970982	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4970984	0.82[ASN][1000 genomes]
rs4970985	0.82[ASN][1000 genomes]
rs4970986	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59024312	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587542	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6658066	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660845	0.80[EUR][1000 genomes]
rs6669855	0.80[EUR][1000 genomes]
rs6677420	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66847267	0.81[ASN][1000 genomes]
rs72704679	0.84[ASN][1000 genomes]
rs72704682	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72704685	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7518156	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752376	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528773	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548516	0.88[ASN][1000 genomes]
rs7556451	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7556661	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8444	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897815	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9661876	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs12067685	RP11-316M1.12	cis	lung	GTEx
rs12067685	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs12067685	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12067685	RP11-316M1.12	cis	Whole Blood	GTEx
rs12067685	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12067685	HORMAD1	cis	Nerve Tibial	GTEx
rs12067685	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs12067685	RP11-316M1.12	cis	Artery Tibial	GTEx
rs12067685	RP11-316M1.12	cis	Thyroid	GTEx
rs12067685	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12067685	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12067685	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12067685	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs12067685	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12067685	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12067685	RP11-316M1.12	cis	Artery Aorta	GTEx
rs12067685	GOLPH3L	cis	Nerve Tibial	GTEx
rs12067685	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12067685	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs12067685	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs12067685	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs12067685	CTSS	cis	Thyroid	GTEx
rs12067685	CTSS	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150950200-150953400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:150950200-150953400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:150950200-150953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:150950200-150953600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:150950200-150953600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:150950200-150953800	Weak transcription	Right Ventricle	heart
7	chr1:150950200-150954200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:150950400-150953400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:150950400-150953600	Weak transcription	HSMMtube	muscle
10	chr1:150951200-150953800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:150952000-150953400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:150952000-150953400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:150952000-150953600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:150952000-150953600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:150952000-150953600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:150952000-150953600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:150952000-150953800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:150952000-150953800	Weak transcription	Gastric	stomach
19	chr1:150952000-150953800	Weak transcription	Lung	lung
20	chr1:150952000-150954000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
22	chr1:150952200-150953400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:150952200-150953800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:150952200-150955000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:150952400-150953400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:150952400-150953400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:150952400-150953400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:150952400-150953400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:150952400-150953600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:150952400-150953600	Weak transcription	NHDF-Ad	bronchial
31	chr1:150952400-150953800	Weak transcription	HSMM	muscle
32	chr1:150952400-150954400	Enhancers	Liver	Liver
33	chr1:150952600-150953200	Weak transcription	HepG2	liver
34	chr1:150952600-150953600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:150952600-150953600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:150952600-150953600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:150952600-150953600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:150952600-150953600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:150952600-150953600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:150952600-150953600	Weak transcription	Fetal Intestine Small	intestine
41	chr1:150952600-150953600	Weak transcription	Fetal Kidney	kidney
42	chr1:150952600-150953600	Weak transcription	Pancreas	Pancrea
43	chr1:150952600-150953600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:150952600-150953600	Weak transcription	Stomach Mucosa	stomach
45	chr1:150952600-150953600	Weak transcription	Thymus	Thymus
46	chr1:150952600-150953600	Weak transcription	K562	blood
47	chr1:150952600-150953600	Weak transcription	NH-A	brain
48	chr1:150952600-150953600	Weak transcription	NHLF	lung
49	chr1:150952600-150953600	Weak transcription	Osteobl	bone
50	chr1:150952600-150953800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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