Variant report

Variant	rs619523
Chromosome Location	chr13:76333701-76333702
allele	A/C
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	1.00[AMR][1000 genomes]
rs2761075	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2761076	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs486860	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs516359	1.00[AMR][1000 genomes]
rs525890	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs526899	1.00[AFR][1000 genomes]
rs527890	1.00[AMR][1000 genomes]
rs538884	1.00[AMR][1000 genomes]
rs545943	0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs588500	1.00[AMR][1000 genomes]
rs592466	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs594666	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs596473	1.00[AMR][1000 genomes]
rs600156	1.00[AFR][1000 genomes]
rs605536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs606853	1.00[AMR][1000 genomes]
rs621351	1.00[AMR][1000 genomes]
rs624802	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs642894	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs645822	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs654431	1.00[AMR][1000 genomes]
rs696777	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs696778	0.90[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
rs619523	FHL1	trans	lymphoblastoid	seeQTL
rs619523	TSPYL5	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76308200-76345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:76322400-76334800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:76323800-76336600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:76323800-76356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76324000-76335200	Weak transcription	NH-A	brain
6	chr13:76324200-76334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76325200-76335200	Weak transcription	Ovary	ovary
8	chr13:76326000-76334600	Weak transcription	Fetal Lung	lung
9	chr13:76327200-76333800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:76327800-76333800	Weak transcription	Fetal Brain Male	brain
11	chr13:76328600-76333800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:76329200-76335600	Weak transcription	Primary B cells from cord blood	blood
13	chr13:76330600-76334400	Genic enhancers	Osteobl	bone
14	chr13:76330600-76334800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:76331400-76334600	Enhancers	NHDF-Ad	bronchial
16	chr13:76331600-76333800	Weak transcription	HSMM	muscle
17	chr13:76331800-76333800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:76331800-76334000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr13:76331800-76334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr13:76331800-76334000	Weak transcription	Fetal Thymus	thymus
21	chr13:76331800-76334600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:76332000-76333800	Weak transcription	Thymus	Thymus
23	chr13:76332000-76334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr13:76332000-76334000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:76332000-76334200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:76332000-76334400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr13:76332000-76336600	Weak transcription	Small Intestine	intestine
28	chr13:76332200-76334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:76332200-76334400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr13:76332400-76334000	Weak transcription	Primary T cells from cord blood	blood
31	chr13:76332400-76334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:76332400-76334000	Weak transcription	NHLF	lung
33	chr13:76332400-76334600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:76332600-76334400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:76332800-76333800	Weak transcription	HSMMtube	muscle
36	chr13:76333000-76334000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:76333200-76333800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:76333200-76333800	Enhancers	Fetal Intestine Small	intestine
39	chr13:76333200-76333800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr13:76333200-76333800	Enhancers	Stomach Mucosa	stomach
41	chr13:76333200-76334000	Enhancers	Gastric	stomach
42	chr13:76333200-76334200	Enhancers	Fetal Intestine Large	intestine
43	chr13:76333400-76333800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:76333400-76333800	Flanking Active TSS	HepG2	liver
45	chr13:76333400-76334200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr13:76333600-76333800	Enhancers	Duodenum Mucosa	Duodenum
47	chr13:76333600-76333800	Weak transcription	Esophagus	oesophagus
48	chr13:76333600-76333800	Enhancers	Hela-S3	cervix
49	chr13:76333600-76334000	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr13:76333600-76334400	Enhancers	Liver	Liver

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