Variant report

Variant	rs60608374
Chromosome Location	chr1:46008913-46008914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
2	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:
3	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
4	chr1:46006129..46009713-chr1:46009736..46013035,4	K562	blood:
5	chr1:46008208..46011176-chr1:46015196..46017542,3	MCF-7	breast:
6	chr1:46007470..46009634-chr1:46048719..46050358,2	K562	blood:

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

Extended variants
information (count: 61 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10789465	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211122	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11211129	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211130	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211135	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211136	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11580609	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11582118	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11802397	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12133294	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12568144	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12729715	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12743512	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2088102	0.80[ASN][1000 genomes]
rs2275276	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2356551	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356553	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2453404	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2934856	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2934859	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991970	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2991971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2991972	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991973	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991974	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991975	0.81[ASN][1000 genomes]
rs2993262	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2993263	0.82[ASN][1000 genomes]
rs3014218	0.83[ASN][1000 genomes]
rs3014219	0.85[ASN][1000 genomes]
rs3014220	0.81[ASN][1000 genomes]
rs35092140	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660861	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4660869	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660876	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs512026	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518365	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523526	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs592214	0.81[ASN][1000 genomes]
rs606542	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs622798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs644915	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661321	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs666720	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs667626	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7526571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526665	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7903	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9147	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs937291	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9429079	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429085	0.81[ASN][1000 genomes]
rs945180	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
rs60608374	CCDC163P	cis	Muscle Skeletal	GTEx
rs60608374	CCDC163P	cis	Heart Left Ventricle	GTEx
rs60608374	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs60608374	CCDC163P	cis	lung	GTEx
rs60608374	GPBP1L1	cis	Whole Blood	GTEx
rs60608374	CCDC163P	cis	Artery Aorta	GTEx
rs60608374	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs60608374	CCDC163P	cis	Thyroid	GTEx
rs60608374	CCDC163P	cis	Esophagus Mucosa	GTEx
rs60608374	CCDC163P	cis	Stomach	GTEx
rs60608374	CCDC163P	cis	Artery Tibial	GTEx
rs60608374	CCDC163P	cis	Esophagus Muscularis	GTEx
rs60608374	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs60608374	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs60608374	CCDC163P	cis	Nerve Tibial	GTEx
rs60608374	CCDC163P	cis	Whole Blood	GTEx
rs60608374	LOC126661	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46000800-46016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46002600-46009600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:46006200-46009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:46006400-46009400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:46006400-46009400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:46006600-46009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:46006800-46009800	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:46006800-46012200	Enhancers	Fetal Intestine Small	intestine
10	chr1:46007000-46009400	Enhancers	Primary B cells from cord blood	blood
11	chr1:46007200-46013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:46007400-46009200	Enhancers	GM12878-XiMat	blood
13	chr1:46007400-46011800	Enhancers	Stomach Mucosa	stomach
14	chr1:46007600-46012000	Enhancers	Fetal Intestine Large	intestine
15	chr1:46007800-46009600	Enhancers	Adipose Nuclei	Adipose
16	chr1:46008000-46010000	Enhancers	K562	blood
17	chr1:46008000-46010200	Weak transcription	Placenta	Placenta
18	chr1:46008200-46009200	Enhancers	Primary T cells from cord blood	blood
19	chr1:46008200-46009200	Enhancers	Dnd41	blood
20	chr1:46008200-46009400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:46008200-46009400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:46008200-46009400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:46008200-46009600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:46008200-46010000	Enhancers	Pancreas	Pancrea
25	chr1:46008200-46010200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:46008200-46010400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:46008200-46011000	Enhancers	Spleen	Spleen
28	chr1:46008200-46011400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr1:46008200-46012200	Enhancers	Fetal Thymus	thymus
30	chr1:46008400-46009200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:46008400-46009200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr1:46008400-46009400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:46008400-46009400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:46008400-46009400	Enhancers	HUVEC	blood vessel
35	chr1:46008400-46009800	Enhancers	Right Atrium	heart
36	chr1:46008400-46011400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:46008600-46009000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:46008600-46009200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:46008600-46009200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:46008600-46009200	Enhancers	Liver	Liver
41	chr1:46008600-46009200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:46008600-46009200	Enhancers	HepG2	liver
43	chr1:46008600-46009200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:46008600-46009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:46008600-46009600	Weak transcription	Lung	lung
46	chr1:46008600-46011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:46008800-46009400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:46008800-46009400	Enhancers	Thymus	Thymus
49	chr1:46008800-46009600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:46008800-46009600	Weak transcription	Colonic Mucosa	Colon

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