Variant report

Variant	rs11739020
Chromosome Location	chr5:96113838-96113839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96105857..96109724-chr5:96110706..96115000,6	K562	blood:
2	chr5:96111607..96114046-chr5:96142076..96144170,2	MCF-7	breast:
3	chr5:96106796..96108975-chr5:96113500..96115025,2	K562	blood:
4	chr5:96111913..96114738-chr5:96142530..96144075,2	MCF-7	breast:
5	chr5:96085971..96089920-chr5:96112582..96114784,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAST-5	chr5:96113354-96115686	NONHSAT102909

Variant related genes	Relation type
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10515246	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10515247	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515248	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515249	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10515250	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11135480	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11738115	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738810	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11740375	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740598	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11741100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11742261	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11743410	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11745157	0.83[EUR][1000 genomes]
rs11746534	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11747148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747896	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11748328	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11748519	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11748795	1.00[CEU][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11749811	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750283	0.87[EUR][1000 genomes]
rs11750464	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750671	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11750934	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12186366	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17401901	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17402639	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17402704	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17405676	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17481334	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17481759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17481856	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17484359	1.00[AFR][1000 genomes]
rs2042386	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3213809	0.83[EUR][1000 genomes]
rs3333	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3334	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3335	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35898772	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3797805	0.83[EUR][1000 genomes]
rs55773007	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55996659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56119802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56213813	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56319744	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56325109	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56395748	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72773905	1.00[AFR][1000 genomes]
rs72773906	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72773912	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72773917	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72773922	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72773923	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72773932	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72773942	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72773947	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72773950	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72773968	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72773969	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72773981	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72773986	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72773989	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773991	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72775807	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72775809	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72775817	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72775818	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11739020	CAST	cis	cerebellum	SCAN
rs11739020	CAST	cis	multi-tissue	Pritchard
rs11739020	PXDN	trans	lymphoblastoid	seeQTL
rs11739020	ERAP1	cis	parietal	SCAN
rs11739020	ARTS-1	cis	multi-tissue	Pritchard
rs11739020	PRSS21	trans	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:96070200-96116400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr5:96071400-96126600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:96072600-96115600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:96073400-96115600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:96075200-96120400	Weak transcription	Fetal Brain Female	brain
9	chr5:96079400-96115600	Strong transcription	HMEC	breast
10	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:96079600-96115400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:96079600-96115600	Strong transcription	NHDF-Ad	bronchial
13	chr5:96079600-96123600	Strong transcription	Placenta	Placenta
14	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:96083800-96116400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:96092800-96126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:96094600-96115600	Strong transcription	HSMM	muscle
21	chr5:96096200-96115800	Strong transcription	NH-A	brain
22	chr5:96096400-96122800	Strong transcription	Primary B cells from cord blood	blood
23	chr5:96096600-96116400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:96097400-96115000	Strong transcription	Fetal Intestine Large	intestine
25	chr5:96097400-96115800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr5:96097400-96118000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr5:96097600-96119200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr5:96097800-96126600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:96098000-96115600	Strong transcription	Osteobl	bone
34	chr5:96098000-96115800	Strong transcription	NHLF	lung
35	chr5:96098000-96116600	Strong transcription	Fetal Muscle Leg	muscle
36	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
38	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
39	chr5:96098200-96122600	Strong transcription	Primary T cells from cord blood	blood
40	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr5:96098400-96118600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:96100000-96116000	Strong transcription	HSMMtube	muscle
43	chr5:96100200-96127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:96101200-96119600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:96104200-96136400	Strong transcription	Dnd41	blood
46	chr5:96104400-96116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:96104800-96114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:96104800-96126600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:96105000-96114000	Weak transcription	Gastric	stomach
50	chr5:96105000-96114800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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