Variant report

Variant	rs4660876
Chromosome Location	chr1:46018720-46018721
allele	A/C
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46014904..46019071-chr1:46034504..46037164,4	K562	blood:
2	chr1:46015708..46018405-chr1:46018570..46020723,2	MCF-7	breast:
3	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
4	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
5	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
6	chr1:45993856..45997631-chr1:46016442..46019336,3	K562	blood:
7	chr1:45974303..45976315-chr1:46016860..46019727,2	K562	blood:
8	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
9	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
10	chr1:46015251..46018245-chr1:46018589..46025048,8	MCF-7	breast:
11	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
12	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000234379	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10789465	0.81[EUR][1000 genomes]
rs11211122	0.80[EUR][1000 genomes]
rs11211129	0.84[EUR][1000 genomes]
rs11211130	0.84[EUR][1000 genomes]
rs11211135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211136	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11580609	0.82[EUR][1000 genomes]
rs11582118	0.80[EUR][1000 genomes]
rs12133294	0.84[EUR][1000 genomes]
rs12568144	0.81[EUR][1000 genomes]
rs12743512	0.80[EUR][1000 genomes]
rs2088102	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2275276	0.82[EUR][1000 genomes]
rs2356551	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356553	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453404	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934856	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2934857	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2934858	0.80[ASN][1000 genomes]
rs2934859	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991970	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991971	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991972	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991973	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991974	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991975	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2993262	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993263	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3014216	0.82[ASN][1000 genomes]
rs3014218	0.91[ASN][1000 genomes]
rs3014219	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3014220	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35092140	0.82[EUR][1000 genomes]
rs4660869	0.83[EUR][1000 genomes]
rs512026	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs518365	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523526	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592214	0.98[ASN][1000 genomes]
rs60608374	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs606542	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622798	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644915	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661321	0.80[EUR][1000 genomes]
rs666720	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs667626	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526571	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7526665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7903	0.82[EUR][1000 genomes]
rs9147	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937291	0.80[EUR][1000 genomes]
rs9429079	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429085	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs945180	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4660876	CCDC163P	cis	Heart Left Ventricle	GTEx
rs4660876	CCDC163P	cis	Stomach	GTEx
rs4660876	MAST2	cis	Artery Tibial	GTEx
rs4660876	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs4660876	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs4660876	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs4660876	CCDC163P	cis	Esophagus Mucosa	GTEx
rs4660876	GPBP1L1	cis	Whole Blood	GTEx
rs4660876	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs4660876	CCDC163P	cis	lung	GTEx
rs4660876	CCDC163P	cis	Nerve Tibial	GTEx
rs4660876	CCDC163P	cis	Esophagus Muscularis	GTEx
rs4660876	CCDC163P	cis	Thyroid	GTEx
rs4660876	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs4660876	CCDC163P	cis	Artery Tibial	GTEx
rs4660876	CCDC163P	cis	Muscle Skeletal	GTEx
rs4660876	CCDC163P	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017000-46025800	Weak transcription	Spleen	Spleen
2	chr1:46017400-46020000	Weak transcription	Ovary	ovary
3	chr1:46017400-46023000	Weak transcription	Psoas Muscle	Psoas
4	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
5	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:46017600-46018800	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:46017800-46019800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:46017800-46020000	Weak transcription	A549	lung
9	chr1:46017800-46021400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:46017800-46023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:46017800-46023000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:46017800-46026800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:46017800-46026800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:46017800-46026800	Weak transcription	HSMMtube	muscle
15	chr1:46017800-46027200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:46017800-46027400	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:46017800-46027400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:46017800-46027400	Weak transcription	Gastric	stomach
19	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:46018000-46018800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:46018000-46019800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:46018000-46021400	Weak transcription	Thymus	Thymus
24	chr1:46018000-46021400	Weak transcription	HSMM	muscle
25	chr1:46018000-46027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:46018200-46019200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:46018200-46019800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:46018200-46019800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:46018200-46020000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:46018200-46020400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:46018200-46022000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:46018200-46022200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:46018200-46023000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:46018400-46019000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:46018400-46019200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:46018400-46019400	Weak transcription	Fetal Thymus	thymus
40	chr1:46018400-46019600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:46018400-46019600	Weak transcription	Left Ventricle	heart
42	chr1:46018400-46019800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:46018400-46019800	Weak transcription	Fetal Brain Female	brain
44	chr1:46018400-46019800	Weak transcription	Placenta	Placenta
45	chr1:46018400-46020000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:46018400-46020000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:46018400-46020000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:46018400-46020000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:46018400-46020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:46018400-46020400	Enhancers	HepG2	liver

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