Variant report

Variant	rs17411479
Chromosome Location	chr9:71842379-71842380
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11793527	1.00[ASN][1000 genomes]
rs17411689	1.00[ASN][1000 genomes]
rs17502850	1.00[ASN][1000 genomes]
rs41316486	1.00[ASN][1000 genomes]
rs62567150	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62570183	1.00[ASN][1000 genomes]
rs7027278	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7046393	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709083	1.00[ASN][1000 genomes]
rs73452903	1.00[ASN][1000 genomes]
rs7875359	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
7	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	20 gene(s)	inside rSNPs	diseases
14	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv1049943	chr9:71834295-71855369	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv525532	chr9:71839039-71843023	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17411479	TJP2	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71807800-71842800	Weak transcription	Small Intestine	intestine
2	chr9:71828000-71866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:71828400-71843000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:71828600-71856600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:71828600-71857600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:71828600-71865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:71828800-71844200	Weak transcription	HSMMtube	muscle
8	chr9:71828800-71851000	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:71828800-71874200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:71830200-71846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:71830400-71842800	Weak transcription	Fetal Thymus	thymus
12	chr9:71830600-71846000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr9:71831000-71846600	Weak transcription	Stomach Mucosa	stomach
14	chr9:71831200-71851200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:71831400-71842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:71831400-71868000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:71831400-71872800	Strong transcription	Liver	Liver
18	chr9:71831600-71842800	Weak transcription	Dnd41	blood
19	chr9:71831600-71863200	Weak transcription	Hela-S3	cervix
20	chr9:71833000-71842400	Weak transcription	Right Atrium	heart
21	chr9:71833200-71842800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:71833200-71844000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:71833400-71842800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:71833600-71850600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:71834600-71851000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr9:71834800-71856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:71836400-71842800	Weak transcription	Spleen	Spleen
28	chr9:71836400-71846400	Weak transcription	Psoas Muscle	Psoas
29	chr9:71836400-71874000	Weak transcription	Fetal Brain Male	brain
30	chr9:71836600-71842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:71837000-71842800	Weak transcription	Thymus	Thymus
32	chr9:71837400-71842800	Weak transcription	Brain Angular Gyrus	brain
33	chr9:71837400-71863000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:71837800-71842800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:71837800-71842800	Weak transcription	Gastric	stomach
36	chr9:71838000-71847800	Weak transcription	Fetal Stomach	stomach
37	chr9:71838000-71861600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:71838600-71857600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr9:71838600-71862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:71838800-71842800	Weak transcription	NHDF-Ad	bronchial
41	chr9:71838800-71854800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:71839000-71842800	Weak transcription	Primary B cells from cord blood	blood
43	chr9:71839000-71857400	Strong transcription	HepG2	liver
44	chr9:71839000-71872600	Strong transcription	Fetal Intestine Large	intestine
45	chr9:71839200-71845800	Strong transcription	NHEK	skin
46	chr9:71839600-71846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:71839600-71863400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:71839800-71842800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:71839800-71845800	Strong transcription	Fetal Lung	lung
50	chr9:71839800-71845800	Strong transcription	Rectal Mucosa Donor 29	rectum

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