Variant report

Variant	rs11583707
Chromosome Location	chr1:150950585-150950586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150949566-150950654	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:150950114..150952556-chr1:150975284..150977893,2	K562	blood:
2	chr1:150550324..150553500-chr1:150948263..150951593,4	MCF-7	breast:
3	chr1:150949558..150951518-chr1:150957213..150958786,2	K562	blood:
4	chr1:150950305..150952431-chr1:150971107..150975123,3	K562	blood:
5	chr1:150897410..150900366-chr1:150947492..150952156,4	K562	blood:
6	chr1:150949543..150951625-chr11:11620473..11621993,2	MCF-7	breast:
7	chr1:150950044..150951710-chr4:104823461..104824979,2	MCF-7	breast:
8	chr1:150950100..150952046-chr1:150977560..150979538,2	MCF-7	breast:
9	chr1:150948646..150951124-chr1:150967629..150969757,2	K562	blood:
10	chr1:150949968..150951775-chr4:104823480..104824982,3	MCF-7	breast:
11	chr1:150950075..150953840-chr1:150979246..150981801,5	K562	blood:
12	chr1:150948448..150951342-chr1:151016605..151018874,2	K562	blood:
13	chr1:150550518..150552449-chr1:150950095..150951828,2	MCF-7	breast:
14	chr1:150950114..150953759-chr1:150976393..150978885,3	K562	blood:
15	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
16	chr1:150835862..150838203-chr1:150950221..150953041,2	K562	blood:
17	chr1:150520324..150522575-chr1:150949260..150951135,2	K562	blood:
18	chr1:150892976..150894840-chr1:150949265..150951717,2	K562	blood:
19	chr1:150950155..150952613-chr1:151029273..151031994,2	MCF-7	breast:
20	chr1:150898449..150900113-chr1:150949703..150951359,2	MCF-7	breast:

No data

Variant related genes	Relation type
ANXA9	TF binding region
CERS2	TF binding region
ENSG00000143409	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000163141	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 22 )

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];0.85[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];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204743	0.84[ASN][1000 genomes]
rs11204747	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204748	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204749	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204750	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579736	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581757	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11589886	0.82[ASN][1000 genomes]
rs12059949	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12067685	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090215	0.85[AMR][1000 genomes];0.86[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	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546376	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972060	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2004903	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2124952	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271076	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272214	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280627	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864882	0.82[ASN][1000 genomes]
rs2867296	0.85[EUR][1000 genomes]
rs34985895	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3843843	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3849279	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4451553	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970928	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970929	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970930	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970931	0.83[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];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970987	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970988	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59024312	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587542	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6658066	0.84[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];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66847267	0.81[ASN][1000 genomes]
rs72704679	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72704682	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72704685	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7518156	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752376	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528773	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548516	0.88[ASN][1000 genomes]
rs7556451	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7556661	0.84[AMR][1000 genomes];0.86[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];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9661876	0.83[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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs11583707	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11583707	RP11-316M1.12	cis	Whole Blood	GTEx
rs11583707	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11583707	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11583707	RP11-316M1.12	cis	Thyroid	GTEx
rs11583707	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11583707	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11583707	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11583707	CTSS	cis	Thyroid	GTEx
rs11583707	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11583707	RP11-316M1.12	cis	lung	GTEx
rs11583707	GOLPH3L	cis	Nerve Tibial	GTEx
rs11583707	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11583707	RP11-316M1.12	cis	Artery Aorta	GTEx
rs11583707	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11583707	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs11583707	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11583707	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11583707	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs11583707	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11583707	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11583707	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150948000-150950600	Enhancers	Fetal Thymus	thymus
2	chr1:150948000-150951600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:150948000-150951600	Weak transcription	Colonic Mucosa	Colon
4	chr1:150948000-150951600	Enhancers	Fetal Intestine Large	intestine
5	chr1:150948000-150951600	Weak transcription	Fetal Kidney	kidney
6	chr1:150948000-150951600	Weak transcription	Ovary	ovary
7	chr1:150948000-150951800	Weak transcription	Psoas Muscle	Psoas
8	chr1:150948000-150952600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:150948000-150952600	Enhancers	Fetal Intestine Small	intestine
10	chr1:150948200-150950600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:150948200-150951400	Weak transcription	Fetal Lung	lung
12	chr1:150948200-150951600	Enhancers	Primary T cells from cord blood	blood
13	chr1:150948200-150951800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:150948200-150952000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:150948600-150950600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:150948600-150950600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:150948600-150951800	Weak transcription	Fetal Brain Female	brain
18	chr1:150948600-150952800	Enhancers	Placenta	Placenta
19	chr1:150948800-150950600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr1:150948800-150950600	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:150948800-150952000	Enhancers	Lung	lung
22	chr1:150949000-150951600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:150949200-150950600	Flanking Active TSS	Hela-S3	cervix
24	chr1:150949200-150951600	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:150949200-150951800	Enhancers	Fetal Stomach	stomach
26	chr1:150949200-150952600	Enhancers	NH-A	brain
27	chr1:150949400-150950600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:150949400-150950600	Enhancers	NHDF-Ad	bronchial
29	chr1:150949600-150950600	Enhancers	NHLF	lung
30	chr1:150949600-150951600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:150950000-150951600	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:150950000-150951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:150950000-150951600	Enhancers	Brain Anterior Caudate	brain
34	chr1:150950000-150951600	Enhancers	Brain Substantia Nigra	brain
35	chr1:150950200-150950600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:150950200-150951000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:150950200-150951000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:150950200-150951400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:150950200-150951400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:150950200-150951400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:150950200-150951400	Enhancers	HepG2	liver
42	chr1:150950200-150951600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:150950200-150951600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:150950200-150951600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:150950200-150951600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:150950200-150951600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:150950200-150951600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:150950200-150951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:150950200-150951600	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:150950200-150951600	Enhancers	Primary T helper cells PMA-I stimulated	--

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