Variant report

Variant	rs7048492
Chromosome Location	chr9:71747960-71747961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71733940..71739343-chr9:71741877..71748941,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10114342	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114369	0.87[EUR][1000 genomes]
rs10114632	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10115134	0.87[EUR][1000 genomes]
rs10115283	0.87[EUR][1000 genomes]
rs10121021	0.82[EUR][1000 genomes]
rs10122932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10124710	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125494	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10217120	0.87[EUR][1000 genomes]
rs10217168	0.87[EUR][1000 genomes]
rs10781420	0.86[EUR][1000 genomes]
rs10781425	0.81[ASN][1000 genomes]
rs10781440	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10781456	0.88[EUR][1000 genomes]
rs10869961	0.88[EUR][1000 genomes]
rs10869975	0.87[EUR][1000 genomes]
rs10869976	0.87[EUR][1000 genomes]
rs11145386	0.96[ASN][1000 genomes]
rs11145391	0.99[ASN][1000 genomes]
rs11145460	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11145463	0.80[EUR][1000 genomes]
rs11145484	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12056979	0.89[EUR][1000 genomes]
rs13283073	0.88[EUR][1000 genomes]
rs13289984	0.88[EUR][1000 genomes]
rs13301644	0.88[EUR][1000 genomes]
rs13302681	0.86[EUR][1000 genomes]
rs1339546	0.88[EUR][1000 genomes]
rs1416738	0.88[EUR][1000 genomes]
rs1934263	0.88[EUR][1000 genomes]
rs2309424	0.87[EUR][1000 genomes]
rs28711298	0.86[EUR][1000 genomes]
rs34883177	0.81[EUR][1000 genomes]
rs34965002	0.82[EUR][1000 genomes]
rs4076287	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4406474	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4416888	0.80[ASN][1000 genomes]
rs4421408	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4592105	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744829	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745622	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4745650	0.88[EUR][1000 genomes]
rs4745656	0.84[EUR][1000 genomes]
rs4745692	0.85[EUR][1000 genomes]
rs59620993	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6420276	0.82[ASN][1000 genomes]
rs6560584	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6560585	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6560589	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024540	0.89[EUR][1000 genomes]
rs7026653	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7029627	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7030146	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7034179	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7034303	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7038833	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7048094	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048095	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048937	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7467352	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7849519	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7850547	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850573	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7855817	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7860277	0.81[ASN][1000 genomes]
rs7862404	0.87[EUR][1000 genomes]
rs7865373	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9314865	0.86[EUR][1000 genomes]
rs953812	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	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
25	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
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv6550	chr9:71714144-71760048	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
28	esv1798602	chr9:71718195-71764191	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7048492	TJP2	cis	Whole Blood	GTEx
rs7048492	TJP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71738000-71778200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:71738200-71748800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:71738200-71752400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:71738200-71757000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:71738200-71770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:71743600-71752800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:71744000-71748400	Enhancers	Aorta	Aorta
8	chr9:71744200-71749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:71745000-71749600	Enhancers	Stomach Mucosa	stomach
10	chr9:71745200-71749000	Enhancers	Right Ventricle	heart
11	chr9:71745400-71748200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:71745400-71748400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:71745400-71748400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr9:71745400-71748400	Enhancers	Psoas Muscle	Psoas
15	chr9:71745400-71748400	Enhancers	Right Atrium	heart
16	chr9:71745400-71748800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:71745400-71749000	Enhancers	HSMMtube	muscle
18	chr9:71745400-71770600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:71745600-71748600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr9:71745600-71748800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:71745800-71750000	Enhancers	Fetal Heart	heart
22	chr9:71746000-71748200	Enhancers	Fetal Intestine Large	intestine
23	chr9:71746000-71749200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:71746000-71751600	Weak transcription	Spleen	Spleen
25	chr9:71746000-71752800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:71746000-71754800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:71746200-71764400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:71746400-71758200	Weak transcription	Brain Anterior Caudate	brain
29	chr9:71746400-71758200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:71746400-71759200	Weak transcription	Brain Angular Gyrus	brain
31	chr9:71746400-71783200	Weak transcription	Small Intestine	intestine
32	chr9:71746600-71748600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:71746800-71749000	Weak transcription	Esophagus	oesophagus
34	chr9:71746800-71749200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr9:71747000-71748400	Genic enhancers	HepG2	liver
36	chr9:71747000-71768600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:71747000-71775600	Weak transcription	Hela-S3	cervix
38	chr9:71747200-71748000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:71747200-71748800	Weak transcription	Fetal Stomach	stomach
40	chr9:71747200-71749200	Weak transcription	Lung	lung
41	chr9:71747200-71749600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:71747200-71749600	Weak transcription	K562	blood
43	chr9:71747200-71750600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:71747200-71751600	Weak transcription	Adipose Nuclei	Adipose
45	chr9:71747200-71757000	Weak transcription	Fetal Lung	lung
46	chr9:71747200-71758200	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:71747200-71764200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:71747200-71764200	Weak transcription	Fetal Kidney	kidney
49	chr9:71747200-71766800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr9:71747200-71769800	Weak transcription	Placenta	Placenta

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