Variant report

Variant	rs321949
Chromosome Location	chr19:52858898-52858899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1961205	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2251559	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs2560979	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321938	0.91[CHB][hapmap]
rs321940	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321941	0.81[LWK][hapmap]
rs321946	0.81[LWK][hapmap]
rs321948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745098	0.82[GIH][hapmap]
rs4802923	0.91[EUR][1000 genomes]
rs4802924	0.91[EUR][1000 genomes]
rs7246724	0.89[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs321949	SYT5	cis	cerebellum	SCAN
rs321949	LILRB2	cis	cerebellum	SCAN
rs321949	PYGL	trans	parietal	SCAN
rs321949	GALP	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
5	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
9	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:52851200-52859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
15	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:52854800-52859400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:52855200-52859000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:52855200-52860600	Strong transcription	Fetal Stomach	stomach
20	chr19:52855400-52859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:52855800-52860400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr19:52856000-52859600	Weak transcription	NHDF-Ad	bronchial
23	chr19:52856400-52861400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:52856600-52859200	Strong transcription	Dnd41	blood
25	chr19:52856600-52859600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr19:52856600-52860600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:52856600-52864200	ZNF genes & repeats	Liver	Liver
28	chr19:52856800-52859000	Strong transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:52856800-52859800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:52856800-52859800	Strong transcription	Colon Smooth Muscle	Colon
31	chr19:52856800-52860400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:52856800-52860400	Strong transcription	Left Ventricle	heart
33	chr19:52856800-52860600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr19:52856800-52861000	Strong transcription	Fetal Lung	lung
35	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
36	chr19:52857000-52859400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:52857000-52859600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:52857000-52859800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr19:52857000-52859800	Strong transcription	Right Ventricle	heart
40	chr19:52857000-52860200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:52857000-52860200	Strong transcription	Fetal Intestine Large	intestine
42	chr19:52857000-52860400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:52857000-52860400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
44	chr19:52857000-52860400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:52857000-52860600	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr19:52857000-52860600	ZNF genes & repeats	Lung	lung
47	chr19:52857000-52860800	Strong transcription	Brain Anterior Caudate	brain
48	chr19:52857000-52861000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:52857200-52859800	ZNF genes & repeats	Small Intestine	intestine
50	chr19:52857200-52860200	Strong transcription	Brain Angular Gyrus	brain

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