Variant report

Variant	rs1566029
Chromosome Location	chr19:18258512-18258513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10401175	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10406361	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10409167	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11669624	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12978339	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12981122	0.82[EUR][1000 genomes]
rs12983325	0.96[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12984330	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2009030	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2072490	0.83[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2267922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2270623	0.96[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2384858	0.97[GIH][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3736328	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808116	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7125	0.81[JPT][hapmap]
rs71332122	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs740688	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs740691	0.96[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8108738	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8112290	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917551	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription 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	27 gene(s)	inside rSNPs	diseases
15	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS 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	37 gene(s)	inside rSNPs	diseases
18	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
19	nsv2429	chr19:18234179-18279381	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
21	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
22	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
23	nsv911254	chr19:18248146-18310678	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
24	nsv911255	chr19:18254876-18282586	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1566029	TM6SF2	cis	cerebellum	SCAN
rs1566029	ZNF714	cis	parietal	SCAN
rs1566029	HSH2D	cis	cerebellum	SCAN
rs1566029	GMIP	cis	cerebellum	SCAN
rs1566029	HAPLN4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18230800-18262000	Weak transcription	Dnd41	blood
2	chr19:18231000-18262200	Weak transcription	HMEC	breast
3	chr19:18231400-18262200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr19:18231400-18262400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:18232000-18262200	Strong transcription	Brain Hippocampus Middle	brain
6	chr19:18232200-18260000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:18232200-18260000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:18232200-18261800	Strong transcription	Fetal Stomach	stomach
9	chr19:18232400-18260600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:18232600-18262200	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr19:18233200-18261800	Strong transcription	Thymus	Thymus
12	chr19:18235400-18261600	Strong transcription	Spleen	Spleen
13	chr19:18235600-18260800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:18238400-18258800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:18238400-18258800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:18238400-18259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:18238400-18259400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:18238400-18261400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:18238600-18259600	Strong transcription	Brain Substantia Nigra	brain
20	chr19:18238600-18259600	Strong transcription	Fetal Muscle Leg	muscle
21	chr19:18238600-18260000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:18238600-18260000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:18238600-18260200	Strong transcription	Fetal Brain Female	brain
24	chr19:18238600-18260600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:18238600-18260600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:18238800-18258800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:18238800-18258800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:18238800-18259000	Strong transcription	Brain Anterior Caudate	brain
29	chr19:18238800-18260000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:18238800-18260200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:18238800-18260600	Strong transcription	Adipose Nuclei	Adipose
32	chr19:18238800-18262400	Strong transcription	Primary T cells from cord blood	blood
33	chr19:18239600-18262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:18241800-18260600	Strong transcription	Lung	lung
35	chr19:18242000-18262800	Weak transcription	HSMM	muscle
36	chr19:18243600-18262400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:18243600-18262400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr19:18243600-18262600	Weak transcription	Fetal Brain Male	brain
39	chr19:18244200-18262600	Weak transcription	Fetal Kidney	kidney
40	chr19:18247000-18261800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:18247000-18262200	Weak transcription	NH-A	brain
42	chr19:18247200-18262200	Weak transcription	A549	lung
43	chr19:18248200-18259200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:18248400-18262400	Strong transcription	Fetal Intestine Small	intestine
45	chr19:18248600-18259400	Strong transcription	Fetal Intestine Large	intestine
46	chr19:18248600-18260200	Weak transcription	Psoas Muscle	Psoas
47	chr19:18248600-18262200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr19:18248600-18262200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:18248600-18262600	Weak transcription	NHEK	skin
50	chr19:18248800-18261800	Strong transcription	Monocytes-CD14+_RO01746	blood

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