Variant report

Variant	rs17590919
Chromosome Location	chr11:19188485-19188486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16936270	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60422114	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73438394	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17590919	SAA3P	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19143400-19201600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:19143600-19197400	Weak transcription	Small Intestine	intestine
3	chr11:19156600-19193200	Weak transcription	Fetal Stomach	stomach
4	chr11:19156800-19193800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:19156800-19194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:19161600-19194400	Weak transcription	HSMM	muscle
7	chr11:19162800-19203000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:19164000-19200400	Weak transcription	Fetal Brain Male	brain
9	chr11:19166400-19203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:19167000-19194200	Weak transcription	Fetal Kidney	kidney
11	chr11:19167400-19194200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:19167800-19199400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:19168000-19201600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:19169000-19189000	Weak transcription	Fetal Intestine Small	intestine
15	chr11:19169000-19194600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:19169400-19197800	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:19169400-19200400	Weak transcription	Brain Angular Gyrus	brain
18	chr11:19170000-19200200	Strong transcription	Primary B cells from cord blood	blood
19	chr11:19171000-19190200	Weak transcription	NH-A	brain
20	chr11:19171600-19192400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:19172200-19208600	Weak transcription	Brain Substantia Nigra	brain
22	chr11:19172800-19194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:19172800-19194400	Weak transcription	Brain Germinal Matrix	brain
24	chr11:19173400-19196800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:19174000-19209000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:19174800-19189800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:19175600-19190600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:19176400-19213400	Weak transcription	Psoas Muscle	Psoas
29	chr11:19176600-19194200	Weak transcription	Pancreas	Pancrea
30	chr11:19176800-19196000	Weak transcription	Right Ventricle	heart
31	chr11:19177800-19192400	Strong transcription	HUVEC	blood vessel
32	chr11:19177800-19199000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:19178200-19199800	Strong transcription	Primary T cells from cord blood	blood
34	chr11:19178800-19194600	Weak transcription	Fetal Lung	lung
35	chr11:19179000-19194200	Weak transcription	Stomach Mucosa	stomach
36	chr11:19179800-19194200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:19181200-19194000	Weak transcription	Liver	Liver
38	chr11:19182600-19196000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:19182600-19199400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:19183200-19193200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:19184600-19196000	Weak transcription	NHLF	lung
42	chr11:19184600-19198800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:19184800-19197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:19184800-19199200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:19184800-19201000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:19185200-19189000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:19185200-19191000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:19185200-19191200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr11:19185200-19194200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:19185200-19198400	Strong transcription	Dnd41	blood

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