Variant report

Variant	rs11665940
Chromosome Location	chr19:19830928-19830929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11085270	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669075	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12608822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs17699261	0.97[ASN][1000 genomes]
rs247777	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247779	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55882648	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56129543	0.96[ASN][1000 genomes]
rs56167115	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57119263	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59067721	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73006714	0.84[AMR][1000 genomes]
rs73006760	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73006763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv519533	chr19:19789528-19831544	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1065704	chr19:19797999-19865818	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
6	nsv543929	chr19:19797999-19865818	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1062017	chr19:19803482-19865818	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv543930	chr19:19803482-19865818	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1057601	chr19:19803482-19873623	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1063535	chr19:19806386-19863631	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1062212	chr19:19806386-19869332	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1060122	chr19:19814678-19879575	Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv2436	chr19:19815858-19869171	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv33937	chr19:19826866-19831655	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11665940	ZNF14	cis	parietal	SCAN
rs11665940	ATP13A1	cis	multi-tissue	Pritchard
rs11665940	ZNF626	cis	lymphoblastoid	seeQTL
rs11665940	ZNF99	cis	parietal	SCAN
rs11665940	SLC27A1	cis	cerebellum	SCAN
rs11665940	ARMC6	cis	cerebellum	SCAN
rs11665940	CYP4F12	cis	cerebellum	SCAN
rs11665940	CALR3	cis	parietal	SCAN
rs11665940	MPV17L2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19811600-19833200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:19813400-19833000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:19814200-19833200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:19814600-19831400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
5	chr19:19814600-19831400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:19814600-19833000	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:19814800-19831400	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:19815800-19831000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
9	chr19:19815800-19833200	ZNF genes & repeats	Brain Hippocampus Middle	brain
10	chr19:19817600-19831000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr19:19817600-19831200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:19817600-19832000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:19817600-19833200	ZNF genes & repeats	Dnd41	blood
14	chr19:19817800-19831200	ZNF genes & repeats	Brain Anterior Caudate	brain
15	chr19:19818000-19831400	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr19:19818400-19833800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:19818600-19832400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:19819200-19831200	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr19:19819200-19831200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:19819200-19831200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr19:19820000-19831200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr19:19820000-19831200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr19:19820000-19833000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
24	chr19:19820600-19831200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr19:19821800-19832600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:19825200-19831000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
27	chr19:19826000-19831000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:19827000-19831600	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr19:19828400-19843200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:19828600-19838200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:19829800-19837800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:19830200-19831000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:19830200-19831000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
34	chr19:19830200-19831200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:19830400-19831200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr19:19830600-19831200	ZNF genes & repeats	Fetal Brain Male	brain
37	chr19:19830600-19831200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
38	chr19:19830800-19831000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
39	chr19:19830800-19831000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
40	chr19:19830800-19831000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:19830800-19831000	ZNF genes & repeats	Fetal Kidney	kidney
42	chr19:19830800-19831000	ZNF genes & repeats	Gastric	stomach
43	chr19:19830800-19831000	ZNF genes & repeats	Pancreas	Pancrea
44	chr19:19830800-19831200	ZNF genes & repeats	Esophagus	oesophagus
45	chr19:19830800-19831200	ZNF genes & repeats	Left Ventricle	heart
46	chr19:19830800-19831200	ZNF genes & repeats	NH-A	brain

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