Variant report

Variant	rs666720
Chromosome Location	chr1:46020795-46020796
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
2	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
3	chr1:46020777..46023245-chr1:46030263..46032996,2	K562	blood:
4	chr1:46013953..46018760-chr1:46019151..46024741,9	K562	blood:
5	chr1:45984572..45987422-chr1:46019368..46021467,2	K562	blood:
6	chr1:46015251..46018245-chr1:46018589..46025048,8	MCF-7	breast:
7	chr1:45477292..45479954-chr1:46019204..46021384,2	K562	blood:
8	chr1:46019905..46021465-chr1:46027471..46029207,2	K562	blood:
9	chr1:46013953..46019415-chr1:46020167..46024741,10	K562	blood:
10	chr1:46020234..46023064-chr1:46033814..46036863,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10430105	0.87[JPT][hapmap]
rs10789463	0.83[CEU][hapmap]
rs10789465	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs10789471	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1084086	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10890334	0.88[JPT][hapmap]
rs10890335	0.87[JPT][hapmap]
rs10890341	0.87[JPT][hapmap]
rs11211129	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11211130	0.83[EUR][1000 genomes]
rs11211135	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211136	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211137	0.84[ASN][1000 genomes]
rs11211139	0.84[ASN][1000 genomes]
rs11211145	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs11211147	0.93[JPT][hapmap]
rs11211149	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs11211152	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs11211160	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs11211161	0.87[JPT][hapmap]
rs11211168	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs11211169	0.87[JPT][hapmap]
rs11211171	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs11211173	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1135812	0.88[JPT][hapmap]
rs11580609	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12023439	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12024590	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12037459	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs12049503	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12077621	0.84[ASN][1000 genomes]
rs12133294	0.83[EUR][1000 genomes]
rs12743512	0.96[CEU][hapmap]
rs1547925	0.87[JPT][hapmap]
rs1972410	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2152078	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2253862	0.87[JPT][hapmap]
rs2275086	0.87[JPT][hapmap]
rs2275276	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2356551	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2356553	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2453404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28370457	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs28550303	0.87[JPT][hapmap]
rs28719889	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs28890893	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2934856	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2934859	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991970	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2991971	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2991972	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991973	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2991974	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991975	0.82[ASN][1000 genomes]
rs2991979	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2991988	0.87[JPT][hapmap]
rs2991989	0.87[JPT][hapmap]
rs2993262	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2993263	0.87[CHB][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3014213	0.83[ASN][1000 genomes]
rs3014220	0.82[ASN][1000 genomes]
rs3014235	0.88[JPT][hapmap]
rs3014237	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3014241	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3014245	0.87[JPT][hapmap]
rs34768551	0.84[ASN][1000 genomes]
rs35092140	0.81[EUR][1000 genomes]
rs3790585	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs3811436	0.87[JPT][hapmap]
rs4439382	0.87[JPT][hapmap]
rs4607935	0.87[JPT][hapmap]
rs4660313	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4660869	0.82[EUR][1000 genomes]
rs4660876	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660880	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs499600	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs512026	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs512083	0.91[ASN][1000 genomes]
rs514595	0.83[ASN][1000 genomes]
rs518365	0.96[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs523526	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592214	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs60608374	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs606542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs622798	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs644915	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6658700	0.87[JPT][hapmap]
rs667626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6694889	0.87[JPT][hapmap]
rs6703748	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7526571	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7526665	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7903	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9147	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937291	0.96[CEU][hapmap]
rs9429079	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9429172	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs945180	0.82[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs666720	CCDC163P	cis	Whole Blood	GTEx
rs666720	CCDC163P	cis	Esophagus Mucosa	GTEx
rs666720	CCDC163P	cis	Heart Left Ventricle	GTEx
rs666720	CCDC163P	cis	Artery Tibial	GTEx
rs666720	CCDC163P	cis	Stomach	GTEx
rs666720	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs666720	Hs.396207	cis	multi-tissue	Pritchard
rs666720	CCDC163P	cis	Muscle Skeletal	GTEx
rs666720	GPBP1L1	cis	Whole Blood	GTEx
rs666720	GPBP1L1	cis	Lymphoblastoid	GTEx
rs666720	AKR1A1	cis	Lymphoblastoid	GTEx
rs666720	MAST2	cis	Artery Tibial	GTEx
rs666720	AKR1A1	cis	multi-tissue	Pritchard
rs666720	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs666720	CCDC163P	cis	lung	GTEx
rs666720	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs666720	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs666720	CCDC163P	cis	Thyroid	GTEx
rs666720	IPP	cis	multi-tissue	Pritchard
rs666720	CCDC163P	cis	Artery Aorta	GTEx
rs666720	CCDC163P	cis	Esophagus Muscularis	GTEx
rs666720	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs666720	CCDC163P	cis	Nerve Tibial	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	chr1:46017400-46023000	Weak transcription	Psoas Muscle	Psoas
3	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
4	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:46017800-46021400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:46017800-46023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:46017800-46023000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:46017800-46026800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:46017800-46026800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:46017800-46026800	Weak transcription	HSMMtube	muscle
11	chr1:46017800-46027200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:46017800-46027400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:46017800-46027400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:46017800-46027400	Weak transcription	Gastric	stomach
15	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:46018000-46021400	Weak transcription	Thymus	Thymus
18	chr1:46018000-46021400	Weak transcription	HSMM	muscle
19	chr1:46018000-46027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:46018200-46022000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:46018200-46022200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:46018200-46023000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:46018400-46020800	Genic enhancers	Fetal Intestine Small	intestine
27	chr1:46018400-46021200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:46018400-46021400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:46018400-46021400	Weak transcription	NH-A	brain
30	chr1:46018400-46022000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:46018400-46022000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:46018400-46022000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:46018400-46022000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:46018400-46022000	Strong transcription	K562	blood
35	chr1:46018400-46022200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:46018400-46022400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:46018400-46022800	Weak transcription	Fetal Heart	heart
38	chr1:46018400-46023000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:46018400-46023000	Weak transcription	Right Atrium	heart
40	chr1:46018400-46023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:46018400-46023000	Weak transcription	Small Intestine	intestine
42	chr1:46018400-46024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:46018400-46025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:46018400-46025800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:46018400-46026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:46018400-46026600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:46018400-46026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:46018400-46026800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:46018400-46027200	Weak transcription	Fetal Lung	lung
50	chr1:46018400-46027400	Weak transcription	Colon Smooth Muscle	Colon

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