Variant report

Variant	rs4744726
Chromosome Location	chr9:71484028-71484029
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71483920..71486082-chr9:71487169..71489754,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10511962	0.83[MEX][hapmap]
rs10869396	0.88[MEX][hapmap]
rs10869400	0.83[MEX][hapmap]
rs10869401	0.87[MEX][hapmap]
rs10869403	0.83[MEX][hapmap]
rs10869419	0.86[ASW][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.84[YRI][hapmap]
rs10869420	0.81[YRI][hapmap]
rs10869432	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10869442	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11144035	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1414944	0.83[MEX][hapmap]
rs1414947	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1414949	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2027205	0.83[YRI][hapmap]
rs2152647	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4237270	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744712	0.86[JPT][hapmap]
rs4745327	0.81[YRI][hapmap]
rs4745328	0.80[YRI][hapmap]
rs4745353	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4745360	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4745366	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6560406	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6560419	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7043133	0.89[CEU][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7043242	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043727	0.86[JPT][hapmap]
rs7043868	0.87[AMR][1000 genomes]
rs7851923	0.81[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs883952	0.92[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744726	TJP2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
3	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
4	chr9:71460400-71495600	Weak transcription	Aorta	Aorta
5	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr9:71463400-71492800	Weak transcription	GM12878-XiMat	blood
7	chr9:71463600-71501800	Weak transcription	Small Intestine	intestine
8	chr9:71467800-71495800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:71468200-71486600	Weak transcription	Left Ventricle	heart
10	chr9:71474600-71492400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:71474800-71501800	Weak transcription	Right Ventricle	heart
12	chr9:71477000-71485600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:71478000-71486000	Strong transcription	Primary B cells from cord blood	blood
14	chr9:71479200-71501600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:71480800-71486200	Weak transcription	Gastric	stomach
16	chr9:71480800-71495600	Weak transcription	Lung	lung
17	chr9:71480800-71495600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:71480800-71501200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:71481000-71485000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr9:71481200-71485600	Weak transcription	HepG2	liver
21	chr9:71481200-71504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:71482000-71492600	Weak transcription	Fetal Intestine Large	intestine
23	chr9:71482400-71495200	Weak transcription	Fetal Intestine Small	intestine
24	chr9:71482600-71486800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr9:71482800-71485200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:71483400-71484200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:71483400-71484800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:71483400-71486800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:71483400-71486800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr9:71483400-71487000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr9:71483400-71487400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr9:71483600-71484200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:71483600-71484600	Enhancers	Fetal Heart	heart
34	chr9:71483600-71484600	Enhancers	Rectal Smooth Muscle	rectum
35	chr9:71483600-71486800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:71483600-71486800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr9:71483600-71487000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:71483800-71484400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr9:71483800-71484400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:71483800-71484400	Enhancers	Colon Smooth Muscle	Colon
41	chr9:71483800-71484600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr9:71483800-71484600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:71483800-71485800	Enhancers	Brain Germinal Matrix	brain
44	chr9:71483800-71487000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:71483800-71487000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:71484000-71484200	Enhancers	Brain Hippocampus Middle	brain
47	chr9:71484000-71484200	Enhancers	Fetal Brain Female	brain
48	chr9:71484000-71484200	Enhancers	Pancreas	Pancrea
49	chr9:71484000-71484400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:71484000-71484400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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