Variant report

Variant	rs518365
Chromosome Location	chr1:46010652-46010653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45986741..45989512-chr1:46009313..46013712,6	MCF-7	breast:
2	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
3	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:
4	chr1:45977514..45980437-chr1:46009344..46010856,2	K562	blood:
5	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
6	chr1:46006129..46009713-chr1:46009736..46013035,4	K562	blood:
7	chr1:46008208..46011176-chr1:46015196..46017542,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10430105	0.82[CHD][hapmap]
rs10749856	0.84[JPT][hapmap]
rs10789463	0.83[TSI][hapmap]
rs10789465	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10789467	0.84[JPT][hapmap]
rs10789470	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1084086	0.85[CHD][hapmap]
rs10890333	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs10890336	0.88[JPT][hapmap]
rs11211122	0.87[EUR][1000 genomes]
rs11211129	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211130	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211135	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211136	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211145	0.87[CHD][hapmap]
rs11211152	0.87[CHD][hapmap]
rs11211157	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11211161	0.82[CHD][hapmap]
rs11211163	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11211166	0.89[JPT][hapmap]
rs11211168	0.87[CHD][hapmap]
rs11211169	0.82[CHD][hapmap]
rs11211171	0.87[CHD][hapmap]
rs11580609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11582118	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11802397	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12024590	0.87[CHD][hapmap]
rs12043945	0.84[JPT][hapmap]
rs12049027	0.81[JPT][hapmap]
rs12091503	0.84[JPT][hapmap]
rs12133294	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12139364	0.91[CHB][hapmap];0.83[MEX][hapmap]
rs1250	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12568144	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12729715	0.85[EUR][1000 genomes]
rs12738318	0.91[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs12743512	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1547924	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs1547925	0.82[CHD][hapmap]
rs1972410	0.87[CHD][hapmap]
rs2050376	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2152078	0.87[CHD][hapmap]
rs2230658	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2230659	0.84[JPT][hapmap]
rs2253862	0.82[CHD][hapmap]
rs2275085	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2275086	0.82[CHD][hapmap]
rs2275276	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2356551	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356553	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453404	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370457	0.87[CHD][hapmap]
rs28375469	0.82[CHD][hapmap]
rs28550303	0.82[CHD][hapmap]
rs28647556	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs28719889	0.87[CHD][hapmap]
rs28817701	0.84[CHD][hapmap]
rs28890893	0.87[CHD][hapmap]
rs2934856	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2934857	0.85[CHD][hapmap]
rs2934859	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991970	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2991971	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991972	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991973	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991974	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2991975	0.85[ASN][1000 genomes]
rs2991979	0.87[CHD][hapmap]
rs2991986	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2991987	0.84[JPT][hapmap]
rs2991988	0.82[CHD][hapmap]
rs2993262	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2993263	0.83[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3013595	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs3013597	0.84[JPT][hapmap]
rs3014210	0.85[CHD][hapmap]
rs3014216	0.85[CHD][hapmap]
rs3014218	0.85[CHD][hapmap]
rs3014219	0.81[ASN][1000 genomes]
rs3014220	0.85[ASN][1000 genomes]
rs3014237	0.87[CHD][hapmap]
rs3014238	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs3014239	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs3014241	0.87[CHD][hapmap]
rs3014242	0.85[CHD][hapmap]
rs3014245	0.82[CHD][hapmap]
rs35092140	0.90[EUR][1000 genomes]
rs3811436	0.82[CHD][hapmap]
rs4431884	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4439382	0.82[CHD][hapmap]
rs4468203	0.83[JPT][hapmap]
rs4559551	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4564187	0.84[JPT][hapmap]
rs4609469	0.84[JPT][hapmap]
rs4660312	0.87[CHD][hapmap]
rs4660313	0.87[CHD][hapmap]
rs4660861	0.82[EUR][1000 genomes]
rs4660869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660876	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660880	0.87[CHD][hapmap]
rs4660882	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs5021934	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs512026	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518216	0.82[CHD][hapmap]
rs523526	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592214	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs60608374	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs606542	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs622798	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644915	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656279	0.84[JPT][hapmap]
rs6658700	0.82[CHD][hapmap]
rs6661321	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs666720	0.96[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs667626	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7526571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7526665	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs781058	0.91[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9147	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937291	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9429079	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs945180	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998199	0.86[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]

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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs518365	FOXD2	cis	parietal	SCAN
rs518365	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs518365	GPBP1L1	cis	Whole Blood	GTEx
rs518365	CCDC163P	cis	Whole Blood	GTEx
rs518365	CCDC163P	cis	Esophagus Mucosa	GTEx
rs518365	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs518365	CCDC163P	cis	lymphoblastoid	seeQTL
rs518365	LOC126661	cis	uninvolved skin	skin_eQTL
rs518365	IPP	cis	lymphoblastoid	seeQTL
rs518365	MMACHC	cis	lymphoblastoid	seeQTL
rs518365	CCDC163P	cis	Muscle Skeletal	GTEx
rs518365	C1orf84	cis	cerebellum	SCAN
rs518365	CCDC163P	cis	Stomach	GTEx
rs518365	CCDC163P	cis	Heart Left Ventricle	GTEx
rs518365	CCDC163P	cis	Artery Tibial	GTEx
rs518365	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs518365	CCDC163P	cis	Nerve Tibial	GTEx
rs518365	TESK2	cis	lymphoblastoid	seeQTL
rs518365	CCDC163P	cis	Thyroid	GTEx
rs518365	CYP4Z2P	cis	cerebellum	SCAN
rs518365	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs518365	CCDC163P	cis	Artery Aorta	GTEx
rs518365	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs518365	TESK2	cis	cerebellum	SCAN
rs518365	CCDC163P	cis	Esophagus Muscularis	GTEx
rs518365	CCDC163P	cis	lung	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46000800-46016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:46006800-46012200	Enhancers	Fetal Intestine Small	intestine
4	chr1:46007200-46013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:46007400-46011800	Enhancers	Stomach Mucosa	stomach
6	chr1:46007600-46012000	Enhancers	Fetal Intestine Large	intestine
7	chr1:46008200-46011000	Enhancers	Spleen	Spleen
8	chr1:46008200-46011400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr1:46008200-46012200	Enhancers	Fetal Thymus	thymus
10	chr1:46008400-46011400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:46008600-46011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:46009200-46010800	Enhancers	Esophagus	oesophagus
13	chr1:46009200-46011000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:46009200-46011400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:46009200-46011400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr1:46009200-46011600	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:46009200-46011800	Flanking Active TSS	HepG2	liver
18	chr1:46009600-46011000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:46009600-46012200	Enhancers	Liver	Liver
20	chr1:46009600-46016000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:46009800-46011000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr1:46010000-46010800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:46010000-46010800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:46010000-46010800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:46010000-46011000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:46010000-46011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:46010000-46011000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:46010000-46011000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:46010000-46011200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:46010000-46011200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:46010000-46011400	Enhancers	Primary T cells from cord blood	blood
32	chr1:46010000-46011400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:46010000-46011400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:46010000-46011400	Enhancers	Adipose Nuclei	Adipose
35	chr1:46010000-46011600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:46010000-46011600	Enhancers	Duodenum Mucosa	Duodenum
37	chr1:46010000-46011600	Enhancers	HUVEC	blood vessel
38	chr1:46010000-46012000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:46010000-46013200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:46010000-46015200	Weak transcription	K562	blood
41	chr1:46010000-46015800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:46010000-46016000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:46010000-46016000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:46010000-46016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:46010000-46016000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:46010000-46016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:46010000-46016000	Weak transcription	Pancreas	Pancrea
48	chr1:46010000-46016000	Weak transcription	Thymus	Thymus
49	chr1:46010000-46016000	Weak transcription	NHLF	lung
50	chr1:46010000-46016000	Weak transcription	Osteobl	bone

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