Variant report

Variant	rs6115011
Chromosome Location	chr20:25022563-25022564
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSX1-4	chr20:25021899-25023358	NONHSAT079123

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs6050267	1.00[ASN][1000 genomes]
rs6076312	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083725	0.89[ASW][hapmap];0.94[CEU][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083726	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083727	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083728	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083729	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115009	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115010	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115013	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217192	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273310	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6115011	MED13L	trans	lymphoblastoid	seeQTL
rs6115011	ADAM23	trans	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
2	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
3	chr20:25013400-25022600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:25014000-25026400	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:25014200-25023000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:25014200-25026400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr20:25014400-25025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:25016200-25023800	Enhancers	Stomach Mucosa	stomach
9	chr20:25016200-25024200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr20:25016200-25024600	Enhancers	Fetal Thymus	thymus
11	chr20:25016400-25024000	Enhancers	Small Intestine	intestine
12	chr20:25016400-25024400	Genic enhancers	Fetal Intestine Small	intestine
13	chr20:25016400-25025800	Enhancers	Fetal Heart	heart
14	chr20:25016600-25023800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr20:25016600-25024600	Enhancers	Pancreas	Pancrea
16	chr20:25016600-25025400	Enhancers	Fetal Muscle Leg	muscle
17	chr20:25016600-25027600	Enhancers	Right Atrium	heart
18	chr20:25016600-25034800	Weak transcription	A549	lung
19	chr20:25017000-25026600	Enhancers	Brain Anterior Caudate	brain
20	chr20:25017400-25026400	Enhancers	Brain Substantia Nigra	brain
21	chr20:25017600-25026400	Enhancers	Left Ventricle	heart
22	chr20:25017800-25023400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr20:25017800-25024400	Enhancers	Lung	lung
24	chr20:25017800-25029000	Genic enhancers	Placenta	Placenta
25	chr20:25017800-25034200	Weak transcription	Fetal Kidney	kidney
26	chr20:25018000-25022600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr20:25018200-25023000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr20:25018200-25024800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:25018400-25024800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr20:25018600-25024600	Enhancers	Fetal Muscle Trunk	muscle
31	chr20:25018600-25025600	Enhancers	Liver	Liver
32	chr20:25018800-25023200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr20:25019600-25023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr20:25019800-25022600	Strong transcription	Dnd41	blood
35	chr20:25020200-25024400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr20:25020200-25026400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr20:25020400-25022800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr20:25020400-25024400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr20:25020600-25022800	Enhancers	Primary T cells from cord blood	blood
40	chr20:25020600-25025000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr20:25020600-25027000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr20:25020600-25037400	Enhancers	Psoas Muscle	Psoas
43	chr20:25021200-25022600	Enhancers	Rectal Smooth Muscle	rectum
44	chr20:25021200-25022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:25021200-25023000	Enhancers	Primary B cells from cord blood	blood
46	chr20:25021200-25023400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr20:25021200-25024600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr20:25021200-25025000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:25021200-25025400	Weak transcription	Fetal Brain Female	brain
50	chr20:25021200-25027200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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