Variant report

Variant	rs2251559
Chromosome Location	chr19:52857399-52857400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1961205	0.92[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2560979	0.92[EUR][1000 genomes]
rs321940	0.91[EUR][1000 genomes]
rs321948	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs321949	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs3745098	0.93[GIH][hapmap];0.85[JPT][hapmap]
rs4802923	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802924	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7246724	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2251559	U2AF2	cis	parietal	SCAN
rs2251559	SYT5	cis	cerebellum	SCAN
rs2251559	ISOC2	cis	cerebellum	SCAN
rs2251559	ZNF132	cis	cerebellum	SCAN
rs2251559	PYGL	trans	parietal	SCAN
rs2251559	LILRB2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
7	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:52848800-52858400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
12	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:52851200-52859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
18	chr19:52852000-52858200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:52852200-52858000	Weak transcription	Fetal Kidney	kidney
20	chr19:52852400-52858400	Weak transcription	Colonic Mucosa	Colon
21	chr19:52852400-52858800	Weak transcription	Fetal Brain Male	brain
22	chr19:52853400-52858400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:52853600-52858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:52854000-52857400	Weak transcription	Brain Substantia Nigra	brain
25	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
27	chr19:52854800-52859400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:52855200-52859000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:52855200-52860600	Strong transcription	Fetal Stomach	stomach
30	chr19:52855400-52858200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:52855400-52859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:52855800-52857400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr19:52855800-52860400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr19:52856000-52858200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:52856000-52858400	Weak transcription	Pancreas	Pancrea
36	chr19:52856000-52858400	Weak transcription	Psoas Muscle	Psoas
37	chr19:52856000-52859600	Weak transcription	NHDF-Ad	bronchial
38	chr19:52856400-52857800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:52856400-52861400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:52856600-52857600	Genic enhancers	Brain Hippocampus Middle	brain
41	chr19:52856600-52858200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:52856600-52859200	Strong transcription	Dnd41	blood
43	chr19:52856600-52859600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
44	chr19:52856600-52860600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:52856600-52864200	ZNF genes & repeats	Liver	Liver
46	chr19:52856800-52857400	Strong transcription	Primary T cells from cord blood	blood
47	chr19:52856800-52857800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:52856800-52857800	ZNF genes & repeats	HSMM	muscle
49	chr19:52856800-52858200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:52856800-52858400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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