Variant report

Variant	rs2351245
Chromosome Location	chr5:95995733-95995734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95994913..95997156-chr5:96000541..96002076,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10045215	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10067766	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10075736	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421911	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs151835	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152014	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152017	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs152020	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs26483	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26484	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.85[ASN][1000 genomes]
rs28093	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs28104	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs31248	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs31249	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[ASN][1000 genomes]
rs4267886	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4590196	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6556937	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6860934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6897588	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7704167	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7705824	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7733671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2351245	CAST	cis	Whole Blood	GTEx
rs2351245	CTC-506B8.1	cis	Whole Blood	GTEx
rs2351245	CTC-506B8.1	cis	Artery Tibial	GTEx
rs2351245	CAST	cis	Nerve Tibial	GTEx
rs2351245	CTC-506B8.1	cis	lung	GTEx
rs2351245	CAST	cis	lung	GTEx
rs2351245	CTC-506B8.1	cis	Esophagus Muscularis	GTEx
rs2351245	CAST	cis	Esophagus Muscularis	GTEx
rs2351245	CTC-506B8.1	cis	Nerve Tibial	GTEx
rs2351245	CAST	cis	Adipose Subcutaneous	GTEx
rs2351245	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs2351245	CAST	cis	Artery Tibial	GTEx
rs2351245	CTC-506B8.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95989000-95996200	Weak transcription	Fetal Lung	lung
2	chr5:95989200-95996400	Weak transcription	Placenta	Placenta
3	chr5:95990000-95996400	Enhancers	Hela-S3	cervix
4	chr5:95990600-95996600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:95991600-95996600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr5:95992200-95996600	Weak transcription	Liver	Liver
7	chr5:95992200-95997600	Weak transcription	Gastric	stomach
8	chr5:95992400-95996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:95992400-95996600	Weak transcription	Small Intestine	intestine
10	chr5:95992400-95996800	Weak transcription	Pancreas	Pancrea
11	chr5:95992400-95997200	Weak transcription	Esophagus	oesophagus
12	chr5:95992600-95995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:95992600-95996000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:95992600-95996200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:95992600-95996800	Weak transcription	Colonic Mucosa	Colon
16	chr5:95992800-95995800	Weak transcription	Stomach Mucosa	stomach
17	chr5:95993000-95995800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr5:95993000-95996200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:95993000-95996400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:95993000-95996400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:95993200-95995800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:95993200-95996200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:95993200-95996200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:95993200-95996200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:95993200-95996200	Enhancers	A549	lung
26	chr5:95993200-95996200	Weak transcription	GM12878-XiMat	blood
27	chr5:95993200-95996400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:95993200-95996400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:95993200-95996600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:95993200-95996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:95993400-95996000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:95993400-95996400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:95993400-95996400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:95993600-95995800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:95993600-95996200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:95993600-95996400	Weak transcription	HUVEC	blood vessel
37	chr5:95993600-95996600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:95993800-95996800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:95993800-95996800	Enhancers	Fetal Intestine Large	intestine
40	chr5:95994000-95995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:95994000-95995800	Weak transcription	NHLF	lung
42	chr5:95994000-95996200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:95994200-95995800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:95994200-95995800	Weak transcription	Osteobl	bone
45	chr5:95994200-95996000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:95994200-95996200	Weak transcription	NH-A	brain
47	chr5:95994200-95996600	Weak transcription	HSMMtube	muscle
48	chr5:95994200-95997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:95994200-95997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:95994400-95996200	Weak transcription	HSMM	muscle

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