Variant report

Variant	rs1752786
Chromosome Location	chr9:97185572-97185573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10821352	0.88[JPT][hapmap]
rs10993181	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1310977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16909983	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs16910109	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs16912862	0.89[CHB][hapmap]
rs1752783	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1769260	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2259463	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265535	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2277182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2479602	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2486600	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2486632	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2769119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2769813	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2769816	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2986834	0.83[ASN][1000 genomes]
rs2986856	1.00[YRI][hapmap]
rs3121031	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131910	0.85[CHB][hapmap]
rs4430150	0.84[EUR][1000 genomes]
rs4436181	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4477096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4559302	0.84[EUR][1000 genomes]
rs4744336	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744338	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4744345	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4744346	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs639276	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6479537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs670230	0.96[CEU][hapmap];0.86[YRI][hapmap]
rs684892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs688165	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7023915	0.80[AFR][1000 genomes]
rs7025755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs7029113	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7031088	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7848227	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7853182	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7860616	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7868530	0.80[EUR][1000 genomes]
rs9299422	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9409511	0.85[CHB][hapmap]
rs9409512	0.85[CHB][hapmap]
rs9409513	0.85[CHB][hapmap]
rs9409530	0.82[EUR][1000 genomes]
rs9409531	0.81[EUR][1000 genomes]
rs9409543	0.81[AMR][1000 genomes]
rs9409546	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9409736	0.81[EUR][1000 genomes]
rs9409748	0.81[EUR][1000 genomes]
rs9409752	0.81[EUR][1000 genomes]
rs9409755	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9409759	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9409765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs9696557	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9696843	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv982324	chr9:97139062-97200156	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1752786	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97158000-97203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:97160400-97203600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
4	chr9:97167800-97203600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:97172000-97186000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:97172000-97203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:97174200-97207000	Weak transcription	Lung	lung
11	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:97175800-97202200	Weak transcription	Dnd41	blood
13	chr9:97176000-97203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:97176200-97192200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:97176200-97194800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:97176200-97195000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:97176200-97201000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:97176200-97203200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:97176200-97203600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:97176200-97203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
22	chr9:97176400-97203200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:97176600-97203400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:97176800-97203200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:97176800-97203600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
27	chr9:97177000-97203200	Weak transcription	Osteobl	bone
28	chr9:97177200-97201000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:97177200-97201000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:97177200-97203600	Weak transcription	Thymus	Thymus
31	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:97177400-97201400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:97177400-97201400	Weak transcription	Fetal Thymus	thymus
34	chr9:97177400-97206400	Weak transcription	Gastric	stomach
35	chr9:97178000-97192400	Weak transcription	Fetal Stomach	stomach
36	chr9:97178000-97203800	Weak transcription	K562	blood
37	chr9:97178200-97201000	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:97178400-97203600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:97178400-97206800	Weak transcription	Esophagus	oesophagus
40	chr9:97179600-97201000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:97179800-97203200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:97180200-97201600	Weak transcription	Primary B cells from cord blood	blood
43	chr9:97180200-97203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:97180400-97201000	Weak transcription	HSMM	muscle
45	chr9:97180400-97203600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:97180600-97201600	Weak transcription	Hela-S3	cervix
47	chr9:97180800-97203200	Weak transcription	GM12878-XiMat	blood
48	chr9:97181000-97204800	Weak transcription	Placenta	Placenta
49	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:97181200-97193200	Weak transcription	Fetal Intestine Small	intestine

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