Variant report

Variant	rs10781479
Chromosome Location	chr9:71816456-71816457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr9:71816311-71816659	HepG2	liver:	n/a	chr9:71816470-71816482
2	HNF4A	chr9:71816133-71816474	HepG2	liver:	n/a	chr9:71816297-71816312 chr9:71816314-71816329
3	FOXA1	chr9:71816331-71816682	HepG2	liver:	n/a	chr9:71816470-71816482

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71733939..71735989-chr9:71814942..71816605,2	MCF-7	breast:

Variant related genes	Relation type
TJP2	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735655	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10869992	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869993	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869994	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10870006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10870012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10870015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10870017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11145627	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11145688	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17062237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309425	0.96[ASN][1000 genomes]
rs2309427	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486449	0.95[ASN][1000 genomes]
rs2498436	0.90[ASN][1000 genomes]
rs2993818	0.91[ASN][1000 genomes]
rs2993819	0.96[ASN][1000 genomes]
rs2993820	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3002377	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3002378	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3002379	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3002380	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3002382	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3750549	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3927676	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4338173	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4576478	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55641500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56226859	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56312702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58264616	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60785288	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61074083	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62567148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6560618	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6560627	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041781	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045103	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048648	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7350225	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850766	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7861292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864775	0.96[ASN][1000 genomes]
rs7873004	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7874888	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs867346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs884428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9410783	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9411195	0.94[ASN][1000 genomes]
rs9411200	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs946540	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10781479	TJP2	cis	Whole Blood	GTEx

Chromatin state (count:78 , 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	chr9:71805000-71817000	Enhancers	Brain Substantia Nigra	brain
6	chr9:71805400-71817000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr9:71806600-71819000	Weak transcription	Fetal Kidney	kidney
8	chr9:71807400-71832200	Weak transcription	Primary T cells from cord blood	blood
9	chr9:71807800-71842800	Weak transcription	Small Intestine	intestine
10	chr9:71808000-71819200	Weak transcription	NHLF	lung
11	chr9:71808200-71819000	Weak transcription	Fetal Stomach	stomach
12	chr9:71808200-71819200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:71809000-71816600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:71810400-71832400	Weak transcription	GM12878-XiMat	blood
15	chr9:71810600-71818800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:71811000-71817200	Enhancers	Brain Hippocampus Middle	brain
17	chr9:71811000-71819000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:71811200-71822400	Weak transcription	Pancreas	Pancrea
19	chr9:71811600-71819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:71812400-71817000	Genic enhancers	HepG2	liver
21	chr9:71813000-71819000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:71813400-71819000	Weak transcription	Placenta	Placenta
23	chr9:71813600-71819200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:71813800-71818800	Weak transcription	Brain Anterior Caudate	brain
25	chr9:71814000-71818800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:71814200-71816600	Enhancers	Lung	lung
27	chr9:71814600-71817000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr9:71814800-71820000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:71814800-71820000	Weak transcription	Psoas Muscle	Psoas
30	chr9:71815000-71818800	Weak transcription	Fetal Lung	lung
31	chr9:71815000-71819000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:71815000-71819000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr9:71815000-71819200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:71815000-71819400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:71815000-71819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:71815000-71830000	Weak transcription	HUVEC	blood vessel
37	chr9:71815200-71832200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:71815400-71818600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:71815400-71818800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:71815400-71818800	Weak transcription	Right Atrium	heart
41	chr9:71815400-71818800	Weak transcription	K562	blood
42	chr9:71815400-71819000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:71815400-71819000	Weak transcription	Stomach Mucosa	stomach
44	chr9:71815400-71819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:71815400-71830000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:71815600-71818000	Weak transcription	Ovary	ovary
47	chr9:71815600-71818800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:71815600-71818800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:71815600-71819000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:71815600-71819200	Weak transcription	Placenta Amnion	Placenta Amnion

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