Variant report

Variant	rs152020
Chromosome Location	chr5:96026085-96026086
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10045215	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10067766	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10075736	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1421911	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs151835	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152014	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152017	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2351245	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	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs26483	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26484	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26485	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs27852	0.92[YRI][hapmap]
rs28040	0.92[ASN][1000 genomes]
rs28093	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs28104	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs31248	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs31249	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4267886	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4590196	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6556937	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6860934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6897588	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7704167	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7705824	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7733671	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs152020	CTC-506B8.1	cis	Whole Blood	GTEx
rs152020	CAST	cis	Nerve Tibial	GTEx
rs152020	CAST	cis	lung	GTEx
rs152020	CTC-506B8.1	cis	Adipose Subcutaneous	GTEx
rs152020	CTC-506B8.1	cis	Artery Tibial	GTEx
rs152020	CAST	cis	Whole Blood	GTEx
rs152020	CAST	cis	Artery Tibial	GTEx
rs152020	CAST	cis	Adipose Subcutaneous	GTEx
rs152020	CAST	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
2	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
3	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
5	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
10	chr5:96004800-96028200	Weak transcription	Lung	lung
11	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:96005000-96038000	Weak transcription	Ovary	ovary
13	chr5:96005000-96038200	Weak transcription	Gastric	stomach
14	chr5:96005600-96027800	Weak transcription	Left Ventricle	heart
15	chr5:96007600-96027800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:96009200-96037600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:96012000-96026400	Weak transcription	NHLF	lung
18	chr5:96013000-96037800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:96013600-96031400	Weak transcription	Stomach Mucosa	stomach
20	chr5:96013800-96037600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:96014000-96030800	Weak transcription	HSMM	muscle
22	chr5:96014800-96027400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:96015400-96031800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:96016200-96031600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:96016600-96035200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:96016800-96027200	Weak transcription	Adipose Nuclei	Adipose
27	chr5:96016800-96027200	Weak transcription	HSMMtube	muscle
28	chr5:96016800-96027800	Weak transcription	Right Atrium	heart
29	chr5:96016800-96035000	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:96016800-96038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:96017000-96034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:96017000-96038000	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:96017200-96027600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:96018800-96038200	Weak transcription	Colonic Mucosa	Colon
35	chr5:96018800-96038200	Weak transcription	Spleen	Spleen
36	chr5:96019000-96026800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:96019000-96031600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:96019400-96026200	Weak transcription	HMEC	breast
39	chr5:96019400-96031600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:96021800-96027800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:96021800-96032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:96022200-96026200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:96022200-96027200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:96022200-96031600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:96022200-96034800	Weak transcription	NH-A	brain
46	chr5:96022400-96031600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:96022600-96027000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:96023000-96027800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:96023000-96030400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:96023000-96035000	Weak transcription	Right Ventricle	heart

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