Variant report

Variant	rs2993262
Chromosome Location	chr1:46013733-46013734
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
2	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
3	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
4	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
5	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
6	chr1:45964110..45966116-chr1:46012244..46013761,2	K562	blood:
7	chr1:46011700..46014598-chr1:46014898..46016779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132780	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	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211136	0.86[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	0.88[ASN][1000 genomes]
rs2275276	0.82[EUR][1000 genomes]
rs2356551	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356553	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453404	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2934857	0.80[ASN][1000 genomes]
rs2934858	0.80[ASN][1000 genomes]
rs2934859	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991970	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991973	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991974	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991975	0.98[ASN][1000 genomes]
rs2993263	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3014216	0.82[ASN][1000 genomes]
rs3014218	0.91[ASN][1000 genomes]
rs3014219	0.93[ASN][1000 genomes]
rs3014220	0.98[ASN][1000 genomes]
rs35092140	0.82[EUR][1000 genomes]
rs4660869	0.83[EUR][1000 genomes]
rs4660876	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512026	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs518365	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523526	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592214	0.98[ASN][1000 genomes]
rs60608374	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs606542	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622798	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644915	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661321	0.80[EUR][1000 genomes]
rs666720	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs667626	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526571	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7526665	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7903	0.82[EUR][1000 genomes]
rs9147	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937291	0.80[EUR][1000 genomes]
rs9429079	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429085	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
rs2993262	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2993262	CCDC163P	cis	Stomach	GTEx
rs2993262	GPBP1L1	cis	Whole Blood	GTEx
rs2993262	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2993262	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs2993262	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2993262	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2993262	CCDC163P	cis	Muscle Skeletal	GTEx
rs2993262	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2993262	CCDC163P	cis	Artery Tibial	GTEx
rs2993262	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2993262	CCDC163P	cis	lung	GTEx
rs2993262	CCDC163P	cis	Nerve Tibial	GTEx
rs2993262	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2993262	CCDC163P	cis	Thyroid	GTEx
rs2993262	CCDC163P	cis	Whole Blood	GTEx
rs2993262	MAST2	cis	Artery Tibial	GTEx

Chromatin state (count:57 , 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	chr1:46009600-46016000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:46010000-46015200	Weak transcription	K562	blood
4	chr1:46010000-46015800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:46010000-46016000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:46010000-46016000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:46010000-46016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:46010000-46016000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:46010000-46016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:46010000-46016000	Weak transcription	Pancreas	Pancrea
11	chr1:46010000-46016000	Weak transcription	Thymus	Thymus
12	chr1:46010000-46016000	Weak transcription	NHLF	lung
13	chr1:46010000-46016000	Weak transcription	Osteobl	bone
14	chr1:46010200-46016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:46010200-46016000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:46010200-46016000	Weak transcription	Fetal Kidney	kidney
17	chr1:46010200-46016200	Weak transcription	Small Intestine	intestine
18	chr1:46010400-46015400	Weak transcription	Dnd41	blood
19	chr1:46010400-46016000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:46010400-46016000	Weak transcription	Lung	lung
21	chr1:46010800-46014000	Weak transcription	Colonic Mucosa	Colon
22	chr1:46010800-46016000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:46010800-46016000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:46010800-46016000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:46011000-46016000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:46011000-46016000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:46011000-46016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:46011200-46016000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:46011200-46016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:46011200-46016000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:46011400-46015400	Weak transcription	Primary T cells from cord blood	blood
32	chr1:46011400-46015800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:46011400-46015800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:46011400-46016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:46011400-46016000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:46011400-46016000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:46011400-46016000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:46011600-46015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:46011600-46015800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:46011600-46015800	Weak transcription	Placenta	Placenta
41	chr1:46011600-46016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:46011600-46016000	Weak transcription	HUVEC	blood vessel
43	chr1:46011800-46015800	Weak transcription	Stomach Mucosa	stomach
44	chr1:46012000-46015600	Weak transcription	Primary B cells from cord blood	blood
45	chr1:46012000-46015800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:46012000-46015800	Weak transcription	HepG2	liver
47	chr1:46012000-46016000	Weak transcription	Fetal Intestine Large	intestine
48	chr1:46012200-46015200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:46012200-46015800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:46012200-46015800	Weak transcription	Fetal Intestine Small	intestine

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