Variant report

Variant	rs9410789
Chromosome Location	chr9:71822472-71822473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71743521..71745547-chr9:71821447..71823888,2	MCF-7	breast:
2	chr9:71812890..71815440-chr9:71822433..71824150,2	MCF-7	breast:
3	chr9:71734287..71736984-chr9:71820853..71823251,4	MCF-7	breast:
4	chr9:71821136..71823802-chr9:71938490..71940529,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10114369	0.94[ASN][1000 genomes]
rs10114632	0.82[ASN][1000 genomes]
rs10115134	0.94[ASN][1000 genomes]
rs10115283	0.92[ASN][1000 genomes]
rs10125494	0.84[ASN][1000 genomes]
rs10217120	0.95[ASN][1000 genomes]
rs10217168	0.95[ASN][1000 genomes]
rs10283782	0.96[ASN][1000 genomes]
rs10781440	0.84[ASN][1000 genomes]
rs10781456	0.91[ASN][1000 genomes]
rs10869956	0.83[ASN][1000 genomes]
rs10869961	0.94[ASN][1000 genomes]
rs10869975	0.95[ASN][1000 genomes]
rs10869976	0.94[ASN][1000 genomes]
rs11145386	0.85[EUR][1000 genomes]
rs11145391	0.85[EUR][1000 genomes]
rs11145460	0.81[ASN][1000 genomes]
rs11145484	0.84[ASN][1000 genomes]
rs11145748	0.96[ASN][1000 genomes]
rs12056979	0.89[ASN][1000 genomes]
rs13283073	0.89[ASN][1000 genomes]
rs13289984	0.89[ASN][1000 genomes]
rs13301644	0.95[ASN][1000 genomes]
rs13302681	0.89[ASN][1000 genomes]
rs1339546	0.95[ASN][1000 genomes]
rs1416738	0.95[ASN][1000 genomes]
rs1538584	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1934263	0.94[ASN][1000 genomes]
rs2309424	0.94[ASN][1000 genomes]
rs2486451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486452	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2498439	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28711298	0.85[ASN][1000 genomes]
rs34872796	0.96[ASN][1000 genomes]
rs34883177	0.98[ASN][1000 genomes]
rs4076287	0.82[ASN][1000 genomes]
rs4406474	0.82[ASN][1000 genomes]
rs4416888	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4421408	0.81[ASN][1000 genomes]
rs4592105	0.82[ASN][1000 genomes]
rs4745650	0.89[ASN][1000 genomes]
rs4745656	0.91[ASN][1000 genomes]
rs4745691	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745692	0.97[ASN][1000 genomes]
rs4745701	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745703	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59620993	0.84[ASN][1000 genomes]
rs7024540	0.95[ASN][1000 genomes]
rs7030146	0.82[ASN][1000 genomes]
rs7043149	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7467352	0.82[ASN][1000 genomes]
rs7849519	0.82[ASN][1000 genomes]
rs7855817	0.82[ASN][1000 genomes]
rs7857404	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7860124	0.87[ASN][1000 genomes]
rs7862404	0.87[ASN][1000 genomes]
rs7865373	0.84[ASN][1000 genomes]
rs9314865	0.94[ASN][1000 genomes]
rs953812	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9410789	TJP2	cis	Whole Blood	GTEx
rs9410789	TJP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71797200-71832000	Weak transcription	Esophagus	oesophagus
4	chr9:71804000-71831800	Weak transcription	Aorta	Aorta
5	chr9:71807400-71832200	Weak transcription	Primary T cells from cord blood	blood
6	chr9:71807800-71842800	Weak transcription	Small Intestine	intestine
7	chr9:71810400-71832400	Weak transcription	GM12878-XiMat	blood
8	chr9:71815000-71830000	Weak transcription	HUVEC	blood vessel
9	chr9:71815200-71832200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:71815400-71830000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:71816000-71831200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:71816600-71822600	Weak transcription	Lung	lung
13	chr9:71816600-71830600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:71816800-71828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:71818600-71822600	Genic enhancers	HepG2	liver
16	chr9:71818800-71823000	Enhancers	K562	blood
17	chr9:71818800-71823400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr9:71819000-71822800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:71819000-71823000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr9:71819000-71824000	Enhancers	Fetal Heart	heart
21	chr9:71819400-71822600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:71819600-71830000	Weak transcription	Fetal Intestine Large	intestine
23	chr9:71819800-71842200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:71820000-71826600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:71820000-71828600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:71820200-71822600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:71820200-71824000	Enhancers	Brain Angular Gyrus	brain
28	chr9:71820200-71826400	Weak transcription	Gastric	stomach
29	chr9:71820200-71828000	Weak transcription	Fetal Intestine Small	intestine
30	chr9:71820200-71828600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:71820200-71831000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:71820200-71831200	Weak transcription	NHEK	skin
33	chr9:71820200-71831800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:71820200-71831800	Weak transcription	Placenta	Placenta
35	chr9:71820200-71832000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:71820200-71832400	Weak transcription	HMEC	breast
37	chr9:71820200-71833000	Weak transcription	HSMM	muscle
38	chr9:71820200-71842200	Weak transcription	NH-A	brain
39	chr9:71820400-71828400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:71820400-71830600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:71820400-71832000	Weak transcription	Osteobl	bone
42	chr9:71820400-71833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:71820400-71840400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:71820400-71842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:71820800-71823000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr9:71820800-71823200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:71820800-71830400	Weak transcription	Fetal Stomach	stomach
48	chr9:71820800-71831200	Weak transcription	NHLF	lung
49	chr9:71820800-71831600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:71820800-71835800	Weak transcription	Psoas Muscle	Psoas

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