Variant report

Variant	rs696778
Chromosome Location	chr13:76356611-76356612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2585628	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2761075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2761076	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs486860	1.00[AMR][1000 genomes]
rs516359	1.00[AMR][1000 genomes]
rs525890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs526899	0.90[AFR][1000 genomes]
rs527890	1.00[AMR][1000 genomes]
rs538884	1.00[AMR][1000 genomes]
rs545943	0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs588500	1.00[AMR][1000 genomes]
rs592466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs594666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs596473	1.00[AMR][1000 genomes]
rs600156	0.90[AFR][1000 genomes]
rs605536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs606853	1.00[AMR][1000 genomes]
rs619523	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs621351	1.00[AMR][1000 genomes]
rs624802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs642894	1.00[AMR][1000 genomes]
rs645822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs654431	1.00[AMR][1000 genomes]
rs696777	1.00[AFR][1000 genomes];1.00[AMR][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	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs696778	TSPYL5	trans	lymphoblastoid	seeQTL
rs696778	FHL1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76338000-76356800	Weak transcription	Brain Anterior Caudate	brain
2	chr13:76338000-76362800	Weak transcription	Fetal Stomach	stomach
3	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
4	chr13:76340000-76363600	Weak transcription	Thymus	Thymus
5	chr13:76342400-76357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:76344800-76356800	Weak transcription	Fetal Lung	lung
8	chr13:76346800-76361600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:76347400-76358000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:76347400-76361400	Weak transcription	HMEC	breast
11	chr13:76347800-76356800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:76347800-76361400	Weak transcription	Gastric	stomach
13	chr13:76349000-76356800	Weak transcription	NHLF	lung
14	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr13:76350200-76358000	Weak transcription	Small Intestine	intestine
16	chr13:76350600-76361200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr13:76351400-76360200	Weak transcription	Right Ventricle	heart
18	chr13:76351800-76356800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:76352800-76357200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:76353400-76362800	Weak transcription	Lung	lung
21	chr13:76353400-76370600	Weak transcription	Primary T cells from cord blood	blood
22	chr13:76353800-76357200	Weak transcription	HepG2	liver
23	chr13:76353800-76357600	Weak transcription	A549	lung
24	chr13:76354800-76357600	Weak transcription	Fetal Intestine Large	intestine
25	chr13:76354800-76358000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr13:76355000-76357600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:76355200-76357400	Weak transcription	Fetal Intestine Small	intestine
28	chr13:76355200-76362400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr13:76355600-76356800	Weak transcription	Esophagus	oesophagus
30	chr13:76355600-76370800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr13:76356200-76358000	Strong transcription	HSMM	muscle
32	chr13:76356400-76357000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:76356400-76357000	Strong transcription	NH-A	brain
34	chr13:76356400-76357200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:76356400-76357200	Genic enhancers	Hela-S3	cervix
36	chr13:76356400-76358200	Genic enhancers	Osteobl	bone
37	chr13:76356600-76357000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:76356600-76357000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr13:76356600-76357000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:76356600-76357000	ZNF genes & repeats	Liver	Liver
41	chr13:76356600-76357000	ZNF genes & repeats	Fetal Kidney	kidney
42	chr13:76356600-76357000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr13:76356600-76357000	ZNF genes & repeats	Left Ventricle	heart
44	chr13:76356600-76357000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
45	chr13:76356600-76357000	ZNF genes & repeats	HSMMtube	muscle
46	chr13:76356600-76357200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:76356600-76357200	ZNF genes & repeats	GM12878-XiMat	blood
48	chr13:76356600-76357400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr13:76356600-76357800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:76356600-76358000	Enhancers	NHDF-Ad	bronchial

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