Variant report

Variant	rs4740872
Chromosome Location	chr9:7105223-7105224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10122120	0.82[YRI][hapmap]
rs10448243	0.90[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10491780	0.82[CEU][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs10758825	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10758826	0.81[YRI][hapmap]
rs10815514	0.81[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs10815525	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10976037	0.82[CEU][hapmap]
rs10976040	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12341169	0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12343146	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13289983	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13292853	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407863	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1407865	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2025324	0.82[YRI][hapmap]
rs3763651	0.82[YRI][hapmap]
rs4742310	0.82[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7042418	0.82[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs717381	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs7849812	0.85[ASW][hapmap];0.82[CEU][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap]
rs7856110	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7858509	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7861286	0.82[CEU][hapmap]
rs7861396	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs7869317	0.84[YRI][hapmap]
rs7871016	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs912204	0.92[YRI][hapmap]
rs9299041	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869932	chr9:7068359-7133384	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892189	chr9:7091968-7150997	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4740872	RANBP6	cis	parietal	SCAN
rs4740872	TPD52L3	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
2	chr9:7075600-7105800	Weak transcription	NHLF	lung
3	chr9:7086600-7105600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:7088800-7128000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:7095400-7107400	Weak transcription	Fetal Kidney	kidney
6	chr9:7098600-7118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:7098800-7108400	Weak transcription	HSMMtube	muscle
8	chr9:7099000-7106800	Weak transcription	Hela-S3	cervix
9	chr9:7100800-7120200	Strong transcription	Primary B cells from cord blood	blood
10	chr9:7102800-7114000	Strong transcription	Primary T cells from cord blood	blood
11	chr9:7103000-7105600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:7103000-7106000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr9:7103000-7110200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:7103000-7148600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:7103200-7105400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:7103200-7105800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:7103200-7106000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:7103200-7108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:7103200-7108200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:7103200-7116200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:7103400-7105400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:7103400-7105400	Enhancers	Psoas Muscle	Psoas
23	chr9:7103400-7105600	Strong transcription	Thymus	Thymus
24	chr9:7103400-7105800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:7103400-7105800	Strong transcription	Liver	Liver
26	chr9:7103400-7105800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:7103400-7106200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:7103400-7107200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:7103600-7105400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:7103600-7105400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:7103600-7105400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr9:7103600-7105600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:7103600-7105600	Strong transcription	Brain Hippocampus Middle	brain
34	chr9:7103600-7105600	Strong transcription	Fetal Intestine Large	intestine
35	chr9:7103600-7105600	Strong transcription	Ovary	ovary
36	chr9:7103600-7105600	Strong transcription	HepG2	liver
37	chr9:7103600-7105800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:7103600-7105800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:7103600-7105800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:7103600-7106000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr9:7103600-7106000	Strong transcription	Dnd41	blood
42	chr9:7103600-7106000	Strong transcription	K562	blood
43	chr9:7103600-7106200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:7103600-7106200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:7103600-7106200	Strong transcription	GM12878-XiMat	blood
46	chr9:7103600-7118600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:7103800-7105600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr9:7103800-7105600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr9:7103800-7105800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:7103800-7106000	Strong transcription	Adipose Nuclei	Adipose

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