Variant report

Variant	rs6587551
Chromosome Location	chr1:150952674-150952675
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	CTCF	chr1:150951358-150952694	MCF-7	breast:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
2	CTCF	chr1:150951495-150952736	A549	lung:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133
3	CTCF	chr1:150951429-150952703	SK-N-SH	brain:	n/a	chr1:150952113-150952122 chr1:150952110-150952128 chr1:150952146-150952162 chr1:150952145-150952163 chr1:150952113-150952126 chr1:150952140-150952161 chr1:150952112-150952133

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	chr1:150457058..150457964-chr1:150951784..150952748,2	K562	blood:
8	chr1:150950075..150953840-chr1:150979246..150981801,5	K562	blood:
9	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
10	chr1:150549116..150552105-chr1:150952338..150954284,2	MCF-7	breast:
11	chr1:150950114..150953759-chr1:150976393..150978885,3	K562	blood:
12	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
13	chr1:150835862..150838203-chr1:150950221..150953041,2	K562	blood:
14	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
15	chr1:150748050..150749658-chr1:150951794..150953371,2	K562	blood:
16	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
17	chr1:150952576..150954333-chr7:75931969..75934548,2	MCF-7	breast:

Variant related genes	Relation type
ANXA9	TF binding region
ENSG00000143384	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000106211	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1081512	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204735	0.81[EUR][1000 genomes]
rs11204737	0.81[EUR][1000 genomes]
rs11204752	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11587718	0.87[ASN][1000 genomes]
rs11587720	0.89[ASN][1000 genomes]
rs12126004	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12402006	0.86[EUR][1000 genomes]
rs12404199	0.86[EUR][1000 genomes]
rs12410050	0.85[EUR][1000 genomes]
rs12758227	0.82[EUR][1000 genomes]
rs1673160	0.87[ASN][1000 genomes]
rs2305814	0.94[ASN][1000 genomes]
rs267735	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754211	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486836	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970932	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7412746	0.82[EUR][1000 genomes]
rs771201	0.87[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs6587551	HORMAD1	cis	Nerve Tibial	GTEx
rs6587551	RP11-316M1.12	cis	lung	GTEx
rs6587551	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs6587551	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6587551	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6587551	RP11-316M1.12	cis	Artery Tibial	GTEx
rs6587551	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6587551	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6587551	CTSS	cis	Thyroid	GTEx
rs6587551	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6587551	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6587551	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6587551	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6587551	RP11-316M1.12	cis	Thyroid	GTEx
rs6587551	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6587551	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6587551	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs6587551	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6587551	RP11-316M1.12	cis	Whole Blood	GTEx
rs6587551	ARNT	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150948600-150952800	Enhancers	Placenta	Placenta
2	chr1:150950200-150952800	Enhancers	HMEC	breast
3	chr1:150950200-150953400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:150950200-150953400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:150950200-150953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:150950200-150953600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150950200-150953600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:150950200-150953800	Weak transcription	Right Ventricle	heart
9	chr1:150950200-150954200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:150950400-150953400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:150950400-150953600	Weak transcription	HSMMtube	muscle
12	chr1:150950600-150952800	Enhancers	Hela-S3	cervix
13	chr1:150951200-150953800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:150951400-150952800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:150951600-150952800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:150951600-150952800	Enhancers	NHEK	skin
17	chr1:150952000-150952800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:150952000-150953400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:150952000-150953400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:150952000-150953600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:150952000-150953600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:150952000-150953600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:150952000-150953600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:150952000-150953800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:150952000-150953800	Weak transcription	Gastric	stomach
26	chr1:150952000-150953800	Weak transcription	Lung	lung
27	chr1:150952000-150954000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
29	chr1:150952200-150952800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:150952200-150952800	Enhancers	Fetal Intestine Large	intestine
31	chr1:150952200-150952800	Enhancers	Fetal Thymus	thymus
32	chr1:150952200-150952800	Enhancers	A549	lung
33	chr1:150952200-150953400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:150952200-150953800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:150952200-150955000	Weak transcription	Brain Germinal Matrix	brain
36	chr1:150952400-150953400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:150952400-150953400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:150952400-150953400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:150952400-150953400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:150952400-150953600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:150952400-150953600	Weak transcription	NHDF-Ad	bronchial
42	chr1:150952400-150953800	Weak transcription	HSMM	muscle
43	chr1:150952400-150954400	Enhancers	Liver	Liver
44	chr1:150952600-150953200	Weak transcription	HepG2	liver
45	chr1:150952600-150953600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:150952600-150953600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:150952600-150953600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:150952600-150953600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:150952600-150953600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:150952600-150953600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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