Variant report

Variant	rs9840346
Chromosome Location	chr3:195011895-195011896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10804414	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1094677	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1105165	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11706264	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12695049	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059843	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13062518	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13072826	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13099106	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13324903	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538767	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2791603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4677834	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4677835	0.86[EUR][1000 genomes]
rs55672262	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927338	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778719	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7633265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634345	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651757	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs823300	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823301	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823302	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823306	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs823310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823311	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs823314	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs931528	0.83[CHB][hapmap]
rs9810077	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
8	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
10	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
11	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
12	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840346	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
3	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
4	chr3:194993000-195012800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:194993000-195020800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:194993000-195021400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
9	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
12	chr3:194993200-195013000	Weak transcription	Hela-S3	cervix
13	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:194996200-195032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:194996400-195033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:194997200-195027400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:194999200-195029400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:195001200-195016400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:195002200-195016600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:195002200-195028200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:195002600-195024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:195002600-195024800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:195002600-195027400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:195003200-195017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:195003400-195014800	Strong transcription	Adipose Nuclei	Adipose
27	chr3:195003400-195016800	Strong transcription	Fetal Thymus	thymus
28	chr3:195003400-195020000	Strong transcription	Primary B cells from cord blood	blood
29	chr3:195003600-195014400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:195003600-195014600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:195003600-195016200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:195003600-195028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:195003800-195018800	Strong transcription	Dnd41	blood
34	chr3:195004000-195017800	Weak transcription	Stomach Mucosa	stomach
35	chr3:195004000-195039600	Weak transcription	Pancreas	Pancrea
36	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
37	chr3:195004200-195039600	Weak transcription	Gastric	stomach
38	chr3:195004400-195021200	Weak transcription	Psoas Muscle	Psoas
39	chr3:195004600-195018800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:195004800-195019000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:195005200-195039600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:195005600-195014600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:195005600-195022800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:195005800-195016200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:195007400-195014600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:195007400-195016200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:195007400-195016400	Weak transcription	A549	lung
48	chr3:195007400-195020000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:195007600-195015600	Weak transcription	HMEC	breast
50	chr3:195007800-195016200	Strong transcription	Placenta	Placenta

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